title: ISRH-seq_salt_rep1


title: ISRH-seq_salt_rep2

status: Public on May 16 2024

type: SRA

city: Nanjing

first: Wu

last: Jing

address: No.1 Weigang, Nanjing, Jiangsu

country: China

institute: Nanjing Agricultural University

library_source: genomic

data_processing:
Sequenced reads were trimmed for adaptor sequences using Fastp
Bowtie2（version 2.2.5）was used for aligning clean reads to the rice reference genome (MSU version7.0) with default parameters
R-loop peak calling was performed using MACS2 (version 2.1.4)
Assembly: MSU v7.0
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak
Library strategy: ISRH-seq

molecule: genomic DNA

organism: Oryza sativa

source_name: seeding

growth_protocol: spread into nutrient soil in the pot or hydroponics for 150 mM NaCl treatment for continuing to grow in the greenhouse at 28-30°C and 14 h/10 h light-dark cycle

extract_protocol:
Purified genomic DNA was fragmented into size as 200-500bp using a sonicator. 100ng, 250ng, 500ng, 3 µg, 5 µg and 8 µg fragmented DNA was used for RNase H in combination with DNA polymerase I for in situ labeling with a total 200 µl reaction at 16℃ for 2h
Streptavidin bound biotin labeled DNA strand was used for single-stranded DNA library preparation using scale ssDNA-seq Lib Prep Kit for Illumina V2 (RK20228, ABclonal Technology, China)

tag: tissue

value: seeding

tag: cell line

tag: cell type

tag: genotype

value: WT

tag: treatment

value: three-day-salt treated


title: ISRH-seq_100ng


title: Med23KO-2

city: Shanghai

first: Lu

last: CHENGJIANG

state: China, Mainland

address: Yueyang Road 320

institute: Shanghai Institute of Biochemistry and Cell Biology

library_source: transcriptomic

data_processing:
The raw reads were assessed with FastQC
The adapter sequences were trimmed with Cutadapt
The trimmed reads were mapped to the mm10 genome with STAR
The RNA expression levels were quantified using FPKM.
Differential gene expression analysis was conducted with cuffdiff
Assembly: mm10
Supplementary files format and content: WT-and-MED23-KO-MuSCs-RNA-seq-3-days-culture.txt

molecule: total RNA

organism: Mus musculus

source_name: skeletal muscle

growth_protocol: FACS-sorted MuSCs were cultured in F10 growth medium (20% FBS, 1% penicillin‒streptomycin (P/S), and 5 ng/ml bFGF (PeproTech #100-18B)) on a type I collagen (Corning #354236)-coated dish

extract_protocol:
RNA extraction by the TRIzol-chloroform-ethanol method
The poly (A) RNA were enriched with oligo (dT) beads and subjected to construct strand-specific DNA libraries using an NEBNext Ultra Directional RNA Library Prep Kit for Illumina.

value: skeletal muscle

value: primary muscle stem cells


title: MT4 -ADPRC -HIV rep1

city: Ceske Budejovice

first: Lenka

last: Gahurova

address: Branisovska 1760

department: Department of molecular biology and genetics

country: Czech Republic

institute: University of South Bohemia

data_processing:
Library strategy: NAD captureSeq
Trimming:  TrimGalore-v0.4.1
Mapping:  Hisat2-v2.1.0
Read count quantification:  Seqmonk-v.1.47.2
Genome_build: GRCh38
Supplementary_files_format_and_content: txt file containing raw read counts of short RNAs (miRNAs, miscRNAs, rRNAs, tRNAs, snRNAs, snoRNAs)

organism: Homo sapiens

source_name: human CD4 + T-cell line MT4

growth_protocol: MT4 cell line was cultured in RPMI 1640 with L-Glutamine and 25 mM Hepes supplemented with 10% FBS, penicillin (100 U/mL) and streptomycin (100 μg/mL) (all Sigma-Aldrich), under standard conditions at 37 °C under a humidified (>90%) atmosphere of 5% CO2/95% air.

extract_protocol:
MT4 cells infected and uninfected were collected by centrifugation (225× g, 5 min, at 20 °C). Cells pellets were washed with PBS and cells were lysed with RNAzol reagent (Sigma-Aldrich). Virus-containing supernatants were filtered (0.45 μm pore size cellulose-acetate filter (VWR)), and stored at −80 °C. HIV-1 titer was measured by 10-fold serial infection of TZM-bl cells (NIH AIDS Reagent Program, Division of AIDS, NIAID, NIH from Dr. John C. Kappes and Dr. Xiaoyun Wu) in triplicate, calculated by Reed-Muench method and expressed as 50% tissue culture infectious dose. Small RNA fraction was purified according to the RNAzol manufacturer’s protocol. The RNA concentration was determined on NanoDrop ONE (ThermoFisher Scientific) and the RNA sample quality control was performed on a 4200 TapeStation System
Briefly, only short fraction of RNA from MT4 cells infected by HIV-1 and MT4 cells not infected was used for the library preparation. The most critical step is the enzyme reaction catalyzed by ADP-ribosylcyclase (ADPRC, Sigma-Aldrich), which is an enzyme specific only for NAD-capped RNA but inactive on canonical RNA. Samples not treated by ADPRC were used as a negative control for non-specifically bound RNA. 100 μg of sRNA for each sample was incubated with 4-pentyn-1-ol (10%) and ADPRC (2.5 ug) in 50 mM Na-HEPES (pH 7.0) and 5 mM MgCl2 for 30 min at 37 °C. The reaction was stopped by phenol/ether extraction and RNA was ethanol precipitated. NAD-capped RNA was then biotinylated (biotin-PEG3-azide, 250 mM) via a copper-catalyzed azide-alkyne cycloaddition (CuAAC) in a freshly prepared mixture of CuSO4 (1 mM), THPTA (0.5 mM) and sodium ascorbate (2 mM) for 30 min at 25 °C, with shaking at 350 r.p.m. The biotinylated RNA was purified by phenol/ether extraction and ethanol precipitated. Mobicol Classic columns (MoBiTec, GmbH) were assembled and 50 μl of streptavidin Sepharose (GE Healthcare) was transferred to each column. After washing the beads by adding three times 200 μL of immobilization buffer (10 mM Na-HEPES, 1 M NaCl and 5 mM EDTA, pH 7.2) to each column and centrifuge at ≥16,100 g for 1 min at rt, the beads were blocked with acetylated BSA (100 μg/ml, Sigma-Aldrich) in 100 uL of immobilization buffer for 20 min at 20 °C, with shaking at 1,000 r.p.m. After three more washes, the RNA was immobilized on the beads for 1 h at 20 °C, with shaking at 1,000 r.p.m. The beads were washed five times with 200 μL of streptavidin wash buffer (50 mM Tris-HCl and 8 M urea, pH 7.4), then equilibrated by washing three times with 200 μL of 1x standard ligation buffer (50 mM Tris-HCl, 10 mM MgCl2, pH 7.4), blocked with acetylated BSA, and washed three more times with 1x standard ligation buffer as described previously. 30 μL of ligation mixture containing adenylated RNA 3′adaptor (5 μM, rApp-CNNNNNNAGATCGGAAGAGCACACGTCTG-(C3)), 1x standard ligation buffer, DMSO (15%, Sigma-Aldrich), acetylated BSA (1.5 μg), 2-mercaptoethanol (50 mM, Sigma-Aldrich), T4 RNA ligase (15 U, Thermo Fisher Scientific), and T4 RNA ligase 2, truncated K227Q(300 U, New England BioLabs) was added to the beads and the mixture was incubate at 4 °C overnight (≥16 h). The biotinylated RNA was rebound by adding 7.5 μL 5 M NaCl and incubated for 1 hour at 20 °C, with shaking at 1,000 r.p.m. After washing the beads five times with the streptavidin wash buffer, they were equilibrated by washing three times with 1× first-strand buffer (50 mM Tris-HCl, 75 mM KCl and 5 mM MgCl2, pH 8.3), blocked with acetylated BSA, and washed another three times with 1× first-strand buffer. The beads were covered with 30 μL of reverse transcription mixture containing dNTPs (0.5 mM each,company), acetylated BSA (1,5 μg), DTT (5 mM), 1x first strand buffer, reverse primer (5 uM, CAGACGTGTGCTCTTCCGAT), and Superscript III reverse transcriptase (300 U) and incubated for 1 hour at 37 °C. The rebinding procedure was repeated and samples were washed five times with streptavidin wash buffer and three times with 1x ExoI buffer (Thermo Scientific). The beads were blocked with acetylated BSA in ExoI buffer and again washed three times with 1x ExoI buffer. The free primers were digested by adding 30 μL of 1x ExoI buffer and 30 U of ExoI (Thermo Scientific) and the mixture was incubated for 30 min at 37 °C. The beads were washed five times with streptavidin wash buffer and three times with immobilization buffer. The RNA was digested by adding 100 μl of 0.15 M NaOH solution and incubating for 25 min at 55 °C. The columns were centrifuged and washed with 100 ul of H2O. The flow-through was ethanol precipitated and the cDNA pellet was dissolved in 19 μl of Terminal deoxynucleotidyl transferase (TdT) tailing mixture containing 1x TdT buffer (Thermo Scientific) and CTP (1.25 mM). After adding 20 U of TdT, the mixture was incubated in thermocycler for 30 min at 37 °C and after the enzyme was thermally denatured by heating to 70 °C for 10 min. Then, the second adaptor was ligated on the cDNA by adding 60 μl of reaction mixture containing 1x standard ligation buffer, cDNA anchor (5 μM each strand, sense: p-CAGATCGGAAGAGCGTCGTGT-(C3), antisense: ACACGACGCTCTTCCGATCTGGG), ATP (10 μM), and T4 DNA ligase (120 Weiss U, Thermo Scientific) and incubating for 16 h at 4 °C.PCR amplification was performed with barcoded PCR primers (Table) in 25 cycles inTaq DNA Pol reaction buffer 1 × (Thermo Scientific), with 1 μM of each barcoded primer, 0.2 mM dNTPs (each) and 2.5 U of DreamTaq DNA Polymerase (Thermo Scientific) in 50 μL of total reaction mixture. Initial denaturation was performed at 95 °C for 3 min, following by annealing for 30 s at 68 °C, elongation for 30 s at 72 °C and denaturation for 30 s at 95 °C. Final extension was performed at 72 °C for 5 min. PCR reaction mixture was loaded on 2.5% agarose gel (140 V for 2 h). Fractions between 100–400 nt were cut and DNA was extracted from the gel by Monarch DNA Gel extraction Kit  (NEB). Multiplexed samples were submitted to the IMG Genomics and Bioinformatics facility for library synthesis using the NextSeq® 500/550 High Output Kit v2, 75 cycles (Illumina) and sequencing on a NextSeq 500/550, Illumina.
NADcapture shortRNA seq

treatment_protocol: MT4 cells were infected with a cell-free HIV-1 strain NL4-3, which was generated by transient transfection of HEK293T cells with a pNL4-3 plasmid (obtained through NIH AIDS Reagent Program, Division of AIDS, NIAID, NIH from Dr. Malcolm Martin). The infected cultures were subsequently expanded by co-cultivation: 48 h post-infection, cell culture supernatants containing viral particles and infected cells were added to uninfected MT-4 cells (5*105 cells per mL) at a ratio of 1:9. The co-culture was synchronized by three successive additions of infected culture supernatant to uninfected MT-4 cells (5*105 cells per mL, the ratio of 1:9, 27 h interval). The cell cultures were incubated for additional 40 hours and then harvested.

value: CD4 + T-cell

tag: infection

value: no HIV-1

value: no ADPRC

tag: sample type

value: control

tag: rna fraction

value: short RNA


title: ISRH-seq_CK(salt)_rep1


title: ZM532, AF, rep2

city: Chengdu

first: Mao

last: Chen

address: Section 4-13, Renmin Rd. South

institute: Biogas Institute of Ministry of Agriculture and Rural Affairs

description:
Hi-C_ZM532_AF_10k.heatmap_ICed.matrix
Hi-C_ZM532_AF_5kb_heatmap.mcool

data_processing:
The Hi-C raw data generated from the Hi-C library were quality filtered using Trimmomatic v0.3882 and the clean data from two replicates were iteratively mapped to the reference genome Z. mobilis ZM4 (https://www.ncbi.nlm.nih.gov/nuccore/NC_006526.2) using the ICE software package.
Dangling ends and other unusable data were filtered, the valid pairs were used to analyze the correlation efficiency of the two biological replicates for each sample using GenomeDISCO. The valid pairs after pooling were binned into 10 kb, 5 kb, or 2 kb nonoverlapping genomic intervals to generate contact maps.
An insulation score algorithm was used to identify the CID boundaries of each sample, as well as the location and numbers of CIDs.
The bacterial chromosome was binned at 5 kb, and the intra-chromosome contacts of each sample were transferred to Fit-Hi-C software. Significant interactions were identified when both the both the p-value and q-value (false discovery rate, FDR) were less than 0.01 and contact count was greater than 2.
Assembly: NC_006526.2
Supplementary files format and content: Contact matrix

organism: Zymomonas mobilis

growth_protocol: Z. mobilis strains were cultured to exponential phase and 10^6 cells were collected by centrifugation at 2,000 g and washed with TE.

extract_protocol:
Cells were then crosslinked with 3% fresh formaldehyde for 30 min at room temperature, followed by 30 min at 4 °C. Formaldehyde was finally quenched with 0.375 M glycine for 20 minutes at 4 °C. Fixed cells were collected, frozen in liquid nitrogen, and stored at -80 °C until use. 1 × 10^9 cells were suspended in 100 μl TE with 2 μl of Ready-Lyse lysozyme (Epicentre), and incubated at room temperature for 20 min before being treated with 0.5% SDS treatment for 10 min at 65 °C. SDS was quenched by adding 50 μl 10% Triton X-100 and incubating it for 15 min at 37 °C. The chromosomal DNA in the cell lysate was then digested for 1 h at 37 °C by adding 50 μl 10x NEB buffer 2.1(NEB), 300μl water, and 100U of Sau3AI. Biotin-14-dCTP (TriLINK) was used to label the restriction fragment ends with biotinylated cytosine nucleotides. Labeled DNA was diluted in a 10.0 ml ligation mix containing 100 Weiss units of T4 DNA ligase (Thermo) and ligated overnight at 16 °C. The crosslinking was reversed overnight at 65°C with 200 μg ml-1 proteinase K (Thermo), and DNA was purified using QIAamp DNA Mini Kit (Qiagen) according to the manufacturer’s instructions. Purified DNA was sheared to a length of ~400 bp.
Biotinylated DNA fragments were pulled down by Dynabeads MyOne Streptavidin C1 beads (Thermo fisher) and prepared for Illumina sequencing by NEBNext Ultra II DNA Library Prep Kit (NEB) as per manufacturer’s instructions. The DNA fragments between 400 and 600 bp were purified and paired-end sequenced on the Illumina HiSeq X Ten platform with 150PE mode.

tag: strain

value: AF


title: ISRH-seq_250ng_rep2


title: ESC2_SCR_Rep3

city: Turin

first: Chiara

last: Cicconetti

state: (TO)

address: Via Nizza, 52

department: Dept. of Life Sciences and Systems Biol

country: Italy

institute: University of Turin

data_processing:
After quality controls with FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/),
raw reads were aligned to the human reference genome (hg38/GRCh38) using STAR 2.7.1a (Dobin et al., 2013) (with parameters –outFilterMismatchNmax 999 –outFilterMismatchNoverLmax 0.04).
Gene expression levels were quantified with featureCounts v1.6.3 (Liao et al., 2014) (options: -t exon -g gene_name) using GENCODE 32 annotation.
Multi-mapped reads were excluded from quantification. Gene expression counts were next analysed using the edgeR package (Robinson et al., 2010).
After low expressed genes filtration (1 count per million (CPM) in less than 3 samples), normalisation factors were calculated using the trimmed-mean of M-values (TMM) method implemented in the calcNormFactors function and CPM were obtained using normalised library sizes.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file of normalized read counts per gene/samples.

extract_protocol:
Total RNA was extracted by using TRIzol Reagents (Invitrogen, 15596026), according to the manufacturer’s protocol.
For library preparation, the quantity and quality of the starting RNA were checked by Qubit and Bioanalyzer (Agilent). 1 μg of total RNA was subjected to poly(A) enrichment and library preparation using the TruSeq® Stranded mRNA Library Prep Kit (Illumina) following the manufacturer’s instructions. Libraries were sequenced on Illumina NextSeq 1000 System (paired-end 60+60 bp reads).

value: Human embryonic stem cell


title: ISRH-seq_250ng_rep1


title: Med23KO-1

description: WT-and-MED23-KO-MuSCs-RNA-seq-3-days-culture.txt


title: Ctrl-3


title: ZM532, AF, rep1


title: ISRH-seq_500ng_rep2


title: Ctrl-2


title: ESC2_SCR_Rep2


title: ISRH-seq_500ng_rep1


title: Ctrl-1


title: zur, RM, rep2

description:
Hi-C_zur_RM_10k.heatmap_ICed.matrix
Hi-C_zur_RM_5kb_heatmap.mcool

source_name: zur

value: zur

value: RM


title: ESC2_SCR_Rep1


title: ZM532, RM, rna-seq, rep2

data_processing:
The raw sequencing data was first subjected to quality control using FraserQC (v1.2) with the default parameters.
Reads were then aligned to Z. mobilis ZM4 reference genome using Bowtie2.
Genes expression levels were quantified by featureCounts of Subread package.
Differentially expressed genes (DEGs) were screened according to the criteria of Foldchange ≥ 2 and FDR < 0.05 by DESeq2. GO enrichment of DEGs was analyzed by clusterProfiler.
Assembly: NC_006526.2
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted using the trizol method and checked on an agarose gel to monitor the degradation and contamination. RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent).
Sequencing libraries were generated from 1 μg total RNA per sample using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB).

value: Genomic mutants


title: ZM532, RM, rep1

description:
Hi-C_ZM532_RM_10k.heatmap_ICed.matrix
Hi-C_ZM532_RM_5kb_heatmap.mcool


title: ISRH-seq_RNaseH


title: ESC2_KD_ZZZ3_Rep3

value: ZZZ3 knockdown


title: ISRH-seq_1μg_rep2


title: DMS273, Erda, rep 8

city: Bethesda

first: Anish

last: Thomas

state: MARYLAND

address: Center for Cancer Research, National Cancer Institute, Building 10 Room 4-5330

department: National Cancer Institute

country: USA

institute: National Institutes of Health

data_processing:
raw RNA-Seq count data were normalized for inter-gene/sample comparison using FPKM, followed by log2(x + 1) transformation, as implemented in the edgeR R/Bioconductor package
Assembly: hg38
Supplementary files format and content: count matrix

source_name: Cell line

growth_protocol: established SCLC cell lines (DMS 273) were grown in RPMI-1640 media supplemented with 10% FBS, Pen-Strep and L-Glutamine at 37˚C and 5% CO2. Cell aliquots were treated with either DMSO or FGFR inhibitor (Erdafitinib) dissolved in DMSO dosed at 3.3 and 33.33uM concentrations once at the beginning of a 5-day interval period. At the end of 5 days, cells were subsequently analyzed for morphological analysis, RNA extraction using standard pipelines for RNA sequencing, and cell lysates preparation for western blot staining.

extract_protocol:
Erdafitinib treated and untreated cells as above were used for RNA extraction after making cell pellets resuspended in 1 mL of TRIzol™ Reagent (Invitrogen) followed by phase separation using chloroform and vigorous shaking. RNA was precipitated used isopropranol (0.5ml per 1ml of Trizol reagen) and washed with 75% ethanol and centrifuged.
RNA-seq libraries were generated using Truseq RNA Access Library Prep Kits (TruSeq RNA Exome kits; Illumina) and sequenced on Highseq3000 sequencers using 75 bp paired-end sequencing method (Illumina, San Diego, CA). For transcriptomic analyses, raw RNA-Seq count data were normalized for inter-gene/sample comparison using FPKM, followed by log2(x + 1) transformation, as implemented in the edgeR R/Bioconductor package

value: Cell line

value: Erdaftinib 33.3 micromolar


title: ESC2_KD_ZZZ3_Rep2


title: ISRH-seq_1μg_rep1

value: seeding

value: WT


title: zur, RM, rep1


title: ZM4, RM, rep2

description:
Hi-C_ZM4_RM_10k.heatmap_ICed.matrix
Hi-C_ZM4_RM_5kb_heatmap.mcool


title: ZM4, RM, rep1


title: ESC2_KD_ZZZ3_Rep1


title: ESC1_SCR_Rep3


title: ISRH-seq_3μg_rep2


title: DMS273, Erda, rep 7


title: ZM532, RM, rep2


title: ISRH-seq_3μg_rep1


title: ESC1_SCR_Rep2


title: ZM532, RM, Zur, rep2

data_processing:
The raw sequencing reads of fastq format were first processed by in-house Perl scripts.
Reads were subsequently checked by FastQC (v1.2) before proceeding with downstream processing.
Clean reads were then mapped to Z. mobilis ZM4 reference genome using Bowtie2 and further subjected to peak calling using MACS2.
The mapping results were visualized using the Integrative Genomics Viewer
Assembly: NC_006526.2
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

growth_protocol: Z. mobilis were grown to an OD600 of 0.6 in RM.

extract_protocol:
Formaldehyde was added to cultures to a final concentration of 1% and cells were crosslinked for 25 min at 30 °C with 100 rpm rotation. Quench formaldehyde was carried out by adding 0.25 M glycine. After crosslink, cells were collected by centrifugation at 4,000 rpm for 10 min and washed twice with 1× ice-cold Phosphate Buffered Saline. The crosslinked pellets were stored at -80 °C until use, or resuspended in 1 ml FA lysis buffer (50 mM Hepes-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS) per 50 ml cultures containing 2 mg ml-1 lysozyme and 1× Protease Inhibitor Cocktail II (Abcam), and then incubated at 37 °C for 30 min to lyse cells. Sonication was used to shred genomic DNA into 200-500 bp fragments, which were then centrifuged at 14,000 rpm for 15 min. The supernatant was retained and either used for immunoprecipitation or stored at -80 °C. Before starting the IP assays, ~ 2% of the supernatant was kept as the input sample, and the remaining extract was pre-cleared with 30 μl agarose protein G beads (CST, 9007s) at 4 °C for 1 h to reduce nonspecific background. The beads can be pelleted by centrifuging at 6,000 rpm for 1 min as per manufacturer’s instructions. 4 μg ml-1 anti-Zur or 10 μg ml-1 anti-Fur monoclonal antibody was added to the supernatant above and incubated at 4 °C overnight. After that, 30 μl agarose protein G beads were added and rocked at 4 °C for 1 h. After centrifugation, the beads were washed twice with 1 ml FA lysis buffer, once with high salt buffer (lysis buffer + 500 mM NaCl), once with LiCl buffer (10 mM Tris, pH 7.5, 1 mM EDTA, 250 mM LiCl, 0.5 % Na deoxycholate), and twice with TE buffer (10 mM Tris, pH 7.5, 1 mM EDTA). Finally, the beads were incubated with 100 μl elution buffer (50 mM Tris, pH 7.5, 10 mM EDTA, 1% SDS) for 20 min at 65 °C and washed once with 150 μl of TE + 0.67% SDS. The supernatant of eluted DNA complexes above was collected and then blended. In addition, 150 μl of TE + 0.67% SDS was added to the input sample. To reverse the crosslinking, all IP and input samples were incubated at 65 °C overnight. After treated with 1 μl of RNase A (10 mg ml-1) and 5 μl of Proteinase K (10 mg ml-1) at 37 °C for 1 h respectively, the immunoprecipitated chromatin was purified using phenol-chloroform-isoamyl alcohol method and resuspend in 50 μl TE buffer pH 7.5.
The DNA-sequencing library was generated by NEBNext Ultra II DNA Library Prep Kit (NEB) as per manufacturer’s instructions and subsequently sequenced on the Illumina HiSeq X Ten platform in 150PE mode.

tag: chip antibody

value: anti-Zur


title: DMS273, Erda, rep 5


title: ESC1_SCR_Rep1


title: DMS273, Control, rep 4

value: Control


title: ISRH-seq_5μg_rep1


title: DMS273, Control, rep 3


title: ZM532, RM, Fur, rep2

value: anti-Fur


title: ISRH-seq_5μg_rep2


title: ISRH-seq_8μg_rep2


title: ESC1_KD_ZZZ3_Rep2


title: ESC1_KD_ZZZ3_Rep3


title: sample_019: Kidney from NVSel strain fish exposed to IHNV at timepoint 4 hrs post challenge

city: Auburn

first: Jason

last: Abernathy

state: AL

address: 990 Wire Road

institute: USDA-ARS

data_processing:
Base-calling and demultiplexing were performed using the native Illumina software by the sequencing service provider.
Raw reads were processed for quality control using fqC v0.11.5 and TrimGalore! software v0.6.4_dev. This software was used to trim low-quality ends from reads, for Illumina adapter removal, and for removal of excess poly(A)-tails.
STAR v2.7.7a was used for alignment of reads to the rainbow trout genome using the default alignment parameters recommended by the STAR software.
Gene counts for reverse-stranded preparations were provided by STAR v2.7.7a using default parameters recommended by the STAR software.
Read counts output from the STAR v2.7.7a software were used to calculate fold-change using the DESeq2 package 1.24.0 in R-BiocManager Release 1.30.10.
Genome_build: All unmasked sequences from the rainbow trout primary assembly in Ensemble (Oncorhynchus_mykiss.Omyk_1.0.dna.primary_assembly)
Supplementary_files_format_and_content: Tab-delimited text files of effective read counts, rounded to the nearest whole number

molecule: polyA RNA

organism: Oncorhynchus mykiss

source_name: Kidney

extract_protocol:
Tissue samples were placed in RNAlater and stored at -80°C until usage. Total RNA was extracted with the Qiagen RNeasy Mini Kit per the manufacturer's recommendation. Total RNA was treated with Amplification Grade DNase I from Sigma-Aldrich and then precipitated prior to library construction.
Library for RNA-Seq was prepared according to KAPA Stranded mRNA-Seq poly-A selected kit with 200-300bp insert size (KAPA Biosystems, Wilmington, MA) using 250 ng total RNAs as input. Final library quality and quantity was analyzed by Agilent Bioanalyzer 2100 and Life Technologies Qubit 3.0 Fluorometer. The RNA integrity was checked by Agilent Bioanalyzer 2100 and samples with clean rRNA peaks were used for further experiments.
RNA-Seq of 150 bp PE (paired end) reads were sequenced on Illumina HiSeq 4000 (Illumina Inc., San Diego, CA).

tag: FISH strain

value: NVSel

tag: pathogen strain

value: IHNV

tag: time post pathogen challenge

value: 4 hrs

value: Kidney


title: ZM532, RM, Fur, rep1


title: ISRH-seq_8μg_rep1


title: DMS273, Control, rep 1


title: ESC1_KD_ZZZ3_Rep1


title: DMS273, Control, rep 2


title: ZM532, RM, INPUT


title: SHH-MB_PDX1, DMSO, 16h, rep2

first: Yi

last: Sui

address: South Chongqing Road

institute: Shanghai Jiao Tong University School of Medicine

description:
160944_DMSO_2
ExVivo_PDX1_JQ1+THZ1+AZD+T531_Count+FPKM.txt

data_processing:
Trim galore was used to automatically detect and trim adapters.
Reads were mapped to GRCh38 or GRCm38 reference genome using Hisat2.
Counts were generated using HTSeq (version 0.11.1).
Assembly: hg38 for Homo sapiens samples, mm10 for Mus musculus samples.
Supplementary files format and content: txt files included raw counts and FPKM for each Sample

source_name: Cells freshly constructed from SHH-subtype medulloblastoma patient-derived xenograft

extract_protocol:
Cells treated with corresponding small molecular inhibitors and mouse cerebellum tissues were harvested and lysed in Trizol. Samples for RNA-seq assays were then sent to MAJORBIO company (Shanghai, China) for RNA extraction.
Samples for RNA-seq assays were sent to MAJORBIO company (Shanghai, China) for library construction and second-generation sequencing.

value: human SHH-subtype medulloblastoma cells

value: 0.1% DMSO treated for 16h


title: ZM532, RM, Zur, rep1


title: PHC [7323C205]

status: Public on May 15 2024

type: RNA

city: Ramat Gan

first: Michael

last: Gurevich

address: Tel Hashomer

department: Multiple Sclerosis Center

country: Israel

institute: Sheba Medical Center

description: PBMC gene expression from PHC patients

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing:
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
Following scanning of the arrays, the microarray raw data were initially normalized by R Bioconductor Packages, all arrays were normalized serially using a single sample microarray normalization approach designed for personal medicine workflows (SCAN Normalization). An empirical Bayes approach (ComBat algorithm) was used to minimize the batch effect in the data

label: biotin

source_name: PBMC from PHC

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: PBMC were purified from  Ficoll hypaque gradient (Invitrogen, USA)

tag: gender

value: Male

tag: age (years)


title: AHC [14659NMS216]

description: PBMC gene expression from AHC patients

source_name: PBMC from AHC


title: AHC [4200ADC210_(HG-U133A_2)]

description: PBMC gene expression from AHC patients

value: Female


title: PHC [6291PDC212]

description: PBMC gene expression from PHC patients


title: PHC [13434PDC213]

description: PBMC gene expression from PHC patients


title: AHC [8600ADC213]

description: PBMC gene expression from AHC patients


title: AHC [5372ADC212]

description: PBMC gene expression from AHC patients


title: PHC [13405C206]

description: PBMC gene expression from PHC patients


title: PHC [13381PDC213]

description: PBMC gene expression from PHC patients


title: PHC [13363PDC212]

description: PBMC gene expression from PHC patients


title: AHC [14520NMS216]

description: PBMC gene expression from AHC patients


title: PHC [6309PDC211]

description: PBMC gene expression from PHC patients


title: PHC [13436PDC211]

description: PBMC gene expression from PHC patients


title: AHC [4549ADC212]

description: PBMC gene expression from AHC patients


title: AHC [7348ADC213]

description: PBMC gene expression from AHC patients


title: PHC [6303PDC210_(HG-U133A_2)]

description: PBMC gene expression from PHC patients


title: AHC [4202ADC211]

description: PBMC gene expression from AHC patients


title: PHC [13406PDC210_(HG-U133A_2)]

description: PBMC gene expression from PHC patients


title: AOMS [14561NMS219]

description: PBMC gene expression from AOMS patients

source_name: PBMC from AOMS


title: AOMS [11283ADMS213]

description: PBMC gene expression from AOMS patients


title: AOMS [7701ADMS213]

description: PBMC gene expression from AOMS patients


title: AOMS [13031TYMS205]

description: PBMC gene expression from AOMS patients


title: AOMS [7618ADMS212]

description: PBMC gene expression from AOMS patients


title: AHC [7669ADC210_(HG-U133A_2)]

description: PBMC gene expression from AHC patients


title: AOMS [14733NMS216]

description: PBMC gene expression from AOMS patients


title: PHC [13380C205]

description: PBMC gene expression from PHC patients


title: AOMS [5219ADMS211]

description: PBMC gene expression from AOMS patients


title: DMS273, Erda, rep 6


title: AOMS [12833ADMS211]

description: PBMC gene expression from AOMS patients


title: AHC [6687ADC211]

description: PBMC gene expression from AHC patients


title: POMS [9469NMS219]

description: PBMC gene expression from POMS patients

source_name: PBMC from POMS


title: AOMS [13429NMS208]

description: PBMC gene expression from AOMS patients


title: AOMS [13546ADMS210_(HG-U133A_2)]

description: PBMC gene expression from AOMS patients


title: AOMS [8071RR157]

description: PBMC gene expression from AOMS patients


title: AOMS [2498CIS150]

description: PBMC gene expression from AOMS patients


title: AOMS [3000OUT98]

description: PBMC gene expression from AOMS patients


title: POMS [14049NMS219]

description: PBMC gene expression from POMS patients


title: POMS [12822PDMS211]

description: PBMC gene expression from POMS patients


title: POMS [3411PDMS211]

description: PBMC gene expression from POMS patients


title: POMS [11727PDMS210_(HG-U133A_2)]

description: PBMC gene expression from POMS patients


title: AOMS [5990ADMS210_(HG-U133A_2)]

description: PBMC gene expression from AOMS patients


title: POMS [12832PDMS204]

description: PBMC gene expression from POMS patients


title: POMS [13324PDMS213]

description: PBMC gene expression from POMS patients


title: POMS [14864NMS216]

description: PBMC gene expression from POMS patients


title: AOMS [7361CIS151]

description: PBMC gene expression from AOMS patients


title: POMS [11088PDMS206]

description: PBMC gene expression from POMS patients


title: POMS [10760PDMS213]

description: PBMC gene expression from POMS patients


title: POMS [12368NMS208]

description: PBMC gene expression from POMS patients


title: POMS [2704PDMS212]

description: PBMC gene expression from POMS patients


title: POMS [13511PDMS210_(HG-U133A_2)]

description: PBMC gene expression from POMS patients


title: POMS [7667PDMS204]

description: PBMC gene expression from POMS patients


title: POMS [2115RR157]

description: PBMC gene expression from POMS patients


title: POMS [4374ONCIS150]

description: PBMC gene expression from POMS patients


title: POMS [13154PDMS206]

description: PBMC gene expression from POMS patients


title: AOMS [5445OUT99]

description: PBMC gene expression from AOMS patients


title: POMS [5777CIS151]

description: PBMC gene expression from POMS patients


title: POMS [9289PDMS205]

description: PBMC gene expression from POMS patients


title: POMS [5152OUT99]

description: PBMC gene expression from POMS patients


title: POMS [1815OUT98]

description: PBMC gene expression from POMS patients


title: POMS [13183PDMS211]

description: PBMC gene expression from POMS patients


title: mouse lung_elastase+LPS_TJ41 rep 1

city: Tokyo

first: Masaaki

last: Yuki

address: 7-3-1 Hongo, Bunkyo-ku Tokyo

department: Respiratory medicine

country: Japan

institute: The University of Tokyo

data_processing:
CLC Genomics Workbench v 21.0.5
RNA-sequencing (RNA-seq) reads were analyzed using CLC Genomics workbench software (Qiagen, Hilden, Germany) .
Read mapping was carried out using HISAT2 against mouse genome mm10.
Differential expression analysis was performed using edgeR Bioconductor package.
Assembly: mm10
Supplementary files format and content: a csv file include normalized values for each sample

source_name: lung

extract_protocol:
Total RNA was extracted according to the instructions of the manufacturer of the RNeasy Mini Kit (Qiagen, Netherlands).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: lung

value: wild type

tag: treatment 1

value: elastase+LPS

tag: treatment 2


title: mouse lung_elastase+LPS_TJ41 rep 2

tag: tissue


title: mouse lung_elastase+LPS_NT rep 1


title: mouse lung_PBS_TJ41 rep 2

value: PBS


title: mouse lung_elastase+LPS_NT rep 2


title: mouse lung_PBS_NT rep 2


title: mouse lung_PBS_NT rep 1


title: Western Diet + CCl4 20

city: Dallas

first: Hao

last: Zhu

state: TX

address: 6000 Harry Hines Blvd.

department: Children’s Research Institute

institute: University of Texas Southwestern Medical Center

data_processing:
The alignment of the reads to the mouse reference genome (GRCm38) was executed using STAR (v2.7.2b), and FeatureCounts (v1.6.4) was employed for gene count quantification.
Assembly: GRCm38
Supplementary files format and content: Comma-delimited text file including raw counts of each sample

source_name: liver

extract_protocol:
Trizol and the Qiagen RNeasy mini kit (#74104).
NuGen Ovation Mouse RNA-Seq Systems 1–16

treatment_protocol: Western Diet + CCl4

value: liver

value: Het + AAV-Cre

value: "Western Diet + CCl4" NASH model for 3 months


title: Western Diet + CCl4 19


title: Western Diet + CCl4 18

value: Homo + AAV-Cre


title: B3

city: Chongqing

first: yuan

last: zhuang

address: Gaotanyan Street

institute: Third Military Medical University

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
clean data were mapped to the reference genome of Homo sapiens from GRCh38 using STRA software (version 2.5.3a) with default parameters.
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKMs were calculated.
Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1). A p-value cutoff of 0.05 and logfold-change cutoff of 0.32 were used to judge the statistical significance of gene expression differences.
Assembly: GRCh38
Supplementary files format and content: tab-delimited excel file includes raw counts for each Sample

source_name: AGS

growth_protocol: AGS cells were cultured in complete RPMI 1640 medium supplemented with 10% FBS in a humidified environment containing 5% CO2 at 37 °C.

extract_protocol:
Total RNAs were extracted  using TRIzol Reagent (Invitrogen, cat. NO 15596026）following the methods by Chomczynski et al (DOI:10.1006/abio.1987.9999).2 μg total RNAs were used for stranded RNA sequencing library
RNA libraries for RNA-seg were prepared using VAHTS Stranded mRNA-seq Library Prep Kit for Illumina V2 (Vazyme Biotech, NR612-02)  following manufacturer's protocols.

treatment_protocol: AGS cells were stimulated with ANGPTL4, cANGPTL4 or nANGPTL4 (1 μg/ml) for 24 h.

tag: cell line

value: AGS

value: gastric epithelial cells

value: ANGPTL4 stimulation


title: C1

tag: cell type

value: nANGPTL4 stimulation


title: C3


title: C2


title: B1


title: A3

value: unstimulated


title: D2

value: cANGPTL4 stimulation


title: D3


title: D1


title: B2


title: MDA-MB-453_5 days_1‰ alcohol_rep2

city: 南京市

first: xinyu

last: wan

state: 江苏省

address: 江苏省南京市鼓楼区华侨路街道汉中路140号南京医科大学北门

institute: Nanjing medical university

hyb_protocol: Cy3 labeled small RNAs were hybridized to Arraystar Human Small RNA Arrays in Agilent Hybridization Oven.

scan_protocol: After washing, the slides were scanned with Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using GeneSpring GX v12.1 software package (Agilent Technologies). After normalization, the probe signals having Present (P) or Marginal (M) QC flags in at least 1 out of 6 samples were retained. Multiple probes from the same small RNA (miRNA/TsRNA (tRF&tiRNA)/pre-miRNA/tRNA/snoRNA) were combined into one RNA level. Differentially expressed small RNAs between two comparison groups were identified by fold change (FC) and statistical significance (p-value) thresholds. Hierarchical Clustering heatmaps, scatter plots, and volcano plots were plotted to display small RNAs expression pattern among samples by R software.

source_name: BRCA cell line,5 days,1‰ alcohol,replicate2

label_protocol: For each sample, 100ng total RNAs were dephosphorylated to form a unified 3-OH end. 3-OH-ended RNA was then denatured by DMSO and enzymatically labeled with Cy3.

growth_protocol: MDA-MB-453 cells were maintained in DMEM supplemented with 10% fetal bovine serum and antibiotics in humidified atmosphere with 5% CO2 in 37℃.

extract_protocol: Total RNA was extracted using TRIzol reagent (Takara) following the manufacturer's protocol. RNA quantity was measured by using NanoDrop ND-1000 spectrophotometer and RNA integrity was assessed by Bioanalyzer 2100 or gel electrophoresis.


title: mouse lung_PBS_TJ41 rep 1

tag: genotype


title: LNCaP_F3_T

city: Taoyuan City

first: I-Hung

last: Shao

address: No. 5, Fuxing St., Guishan Dist.

country: Taiwan

institute: Chang Gung Memorial Hospital

data_processing:
The raw data undergoes a sequencing quality check using FastQC to ensure usability, followed by processing with Trimmomatic to filter out sequences that don't meet quality standards, thereby obtaining high-quality clean reads.
Clean sequences are then mapped to a reference genome, such as GRCh38, using HISAT2, and quantified using featureCount. Subsequently, the mapping results are verified for quality and accuracy through content checks using RSeQC and Qualimap.
Expression levels are calculated using TPM (Transcripts Per Million) and FPKM (Fragments Per Kilobase of transcript per Million mapped reads). Differential gene analysis is conducted using edgeR for normalization, followed by DEGseq for filtering differential genes. Additionally, sample comparisons are performed by examining the correlation coefficients between samples to assess the degree of variation.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: LNCaP

growth_protocol: The human PCa cell lines LNCaP was obtained from the American Type Culture Collection (ATCC, Manassas, VA, USA). The LNCaP cells were maintained in RPMI 1640 medium (Gibco) supplemented with 2 mM L-glutamine, 100 U/mL penicillin, 100 μg/mL streptomycin, 1 mM sodium pyruvate, and 10% fetal bovine serum (FBS; Gibco).

extract_protocol:
RNA was extracted from the LNCaP cells cultured in control-CM, PPAT-CM, or PVAT-CM by using the RNeasy mini kit (Qiagen, Valencia, CA, USA) in accordance with the manufacturer’s instructions.
RNA-Seq libraries were prepared using 1μg of total RNA with the KAPA mRNA HyperPrep Kit (KAPA Biosystems, Roche, Basel, Switzerland) following the manufacturer’s recommendations.

treatment_protocol: The cells were seeded on 6-well plates (Corning, CA, USA) at a density of 3 × 105 cells/well and incubated for 24 h in complete medium. Subsequently, the spent medium was replaced with fresh serum-free medium containing 50% control-CM, PPAT-CM (tumor), or PVAT-CM (normal) with 2% FBS. The cells were incubated at 37ºC for 72 h.

value: LNCaP

value: prostate cancer cell line

tag: treatment

value: culturerd in PPAT-CM


title: LNCaP_F3_C

value: culturerd in control-CM


title: MDA-MB-453_5 days_1‰ alcohol_rep3

address: 江苏省南京市鼓楼区华侨路街道汉中路140号南京医科大学北门

source_name: BRCA cell line,5 days,1‰ alcohol,replicate3


title: MDA-MB-453_5 days_25(OH)D_rep1

address: 江苏省南京市鼓楼区华侨路街道汉中路140号南京医科大学北门

source_name: BRCA cell line,5 days,25(OH)D,replicate1


title: A2


title: MDA-MB-453_5 days_1‰ alcohol_rep1

address: 江苏省南京市鼓楼区华侨路街道汉中路140号南京医科大学北门

source_name: BRCA cell line,5 days,1‰ alcohol,replicate1


title: Western Diet + CCl4 17


title: A1


title: LNCaP_F3_N

value: culturerd in PVAT-CM


title: MDA-MB-453_5 days_25(OH)D_rep3

address: 江苏省南京市鼓楼区华侨路街道汉中路140号南京医科大学北门

source_name: BRCA cell line,5 days,25(OH)D,replicate3


title: Western Diet + CCl4 16


title: MDA-MB-453_5 days_25(OH)D_rep2

address: 江苏省南京市鼓楼区华侨路街道汉中路140号南京医科大学北门

source_name: BRCA cell line,5 days,25(OH)D,replicate2


title: Donor #27

city: Chicago

first: Elnur

last: Babayev

state: IL

address: 303 E Superior St 10-220

department: Obstetrics and Gynecology

institute: Northwestern University

description:
S4, 2 x 150 bp, lane (2000-2500  M read pairs)
DG-38_Donor_27

data_processing:
The quality of reads, in FASTQ format, was evaluated using FastQC. Reads were trimmed to remove Illumina adapters from the 3’ ends using cutadapt (Spencer et al., 2007b).
Trimmed reads were aligned to the Homo sapiens genome (hg38) using STAR (Dobin et al., 2013).
Read counts for each gene were calculated using htseq-count (Anders et al., 2015), and in conjunction with a gene annotation file consisted of 58396 genes for hg38 obtained from Ensembl (Martin et al., 2023).
Normalization and differential expression were calculated using DESeq2 which employs the Wald test (Love et al., 2014).
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include normalized counts for each sample

source_name: adult oocyte donor

extract_protocol:
RNA was extracted using RNeasy Micro Kit [Qiagen, Cat #74004]
Extracted RNA was quantified with a Qubit fluorometer (Cat #Q33238, Thermo Fisher Scientific), and RNA quality control was performed with a Bioanalyzer RNA 6000 Pico Chip (Cat #5067-1513, Agilent Technologies, CA). Samples with an RNA Integrity Number (RIN) >7 passed quality control and were used for library preparation with the Illumina Stranded mRNA Library Prep Kit according to manufacturer’s instructions (Cat #20040532, Illumina Inc., San Diego, CA). This procedure includes mRNA purification and fragmentation, cDNA synthesis, 3’ end adenylation, Illumina adapter ligation, library PCR amplification and validation.

value: Primary Cells

value: Human primary cumulus cells

tag: developmental stage

value: adult


title: Western Diet + CCl4 14

value: liver

value: Het + AAV-Cre


title: Donor #26

description:
S4, 2 x 150 bp, lane (2000-2500  M read pairs)
DG-37_Donor_26


title: Western Diet + CCl4 10

value: Homo + AAV-Cre

value: "Western Diet + CCl4" NASH model for 3 months


title: Western Diet + CCl4 13

value: WT + AAV-Cre


title: Western Diet + CCl4 9


title: Donor #21

description:
S4, 2 x 150 bp, lane (2000-2500  M read pairs)
DG-34_Donor_21


title: Donor #20

description:
S4, 2 x 150 bp, lane (2000-2500  M read pairs)
DG-33_Donor_20


title: Donor #12

description:
S4, 2 x 150 bp, lane (2000-2500  M read pairs)
DG-29_Donor_12


title: Western Diet + CCl4 6


title: Western Diet + CCl4 7


title: Donor #23

description:
S4, 2 x 150 bp, lane (2000-2500  M read pairs)
DG-36_Donor_23


title: Western Diet + CCl4 11


title: Western Diet + CCl4 12


title: Donor #14

description:
S4, 2 x 150 bp, lane (2000-2500  M read pairs)
DG-30_Donor_14


title: Donor #7

description:
S4, 2 x 150 bp, lane (2000-2500  M read pairs)
DG-27_Donor_7


title: Donor #9

description:
S4, 2 x 150 bp, lane (2000-2500  M read pairs)
DG-28_Donor_9


title: Donor #18

description:
S4, 2 x 150 bp, lane (2000-2500  M read pairs)
DG-32_Donor_18


title: Western Diet + CCl4 1


title: Donor #28

description:
S4, 2 x 150 bp, lane (2000-2500  M read pairs)
DG-39_Donor_28


title: Donor #6

description:
S4, 2 x 150 bp, lane (2000-2500  M read pairs)
DG-26_Donor_6


title: Western Diet + CCl4 15


title: Donor #5

description:
S4, 2 x 150 bp, lane (2000-2500  M read pairs)
DG-25_Donor_5


title: Western Diet + CCl4 3


title: Normal Chow Diet 14

data_processing:
RNA-seq data was analyzed with nf-core/rnaseq (v3.14.0) pipeline. Default parameters were employed.
STAR was used to map the raw FastQ reads to the reference genome. Salmon was used to perform gene/transcript quantification.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text file with raw counts for each sample

treatment_protocol: Normal Chow Diet

value: Littermate Pkd1 Homo Cre BL 4

value: Normal Chow Diet


title: Western Diet + CCl4 2


title: Donor #4

description:
S4, 2 x 150 bp, lane (2000-2500  M read pairs)
DG-24_Donor_4


title: Donor #22

description:
S4, 2 x 150 bp, lane (2000-2500  M read pairs)
DG-35_Donor_22


title: Donor #3

description:
S4, 2 x 150 bp, lane (2000-2500  M read pairs)
DG-23_Donor_3


title: Donor #15

description:
S4, 2 x 150 bp, lane (2000-2500  M read pairs)
DG-31_Donor_15


title: Normal Chow Diet 12

value: Littermate Pkd1 Het Cre BL 4


title: Western Diet + CCl4 8


title: Western Diet + CCl4 4


title: Normal Chow Diet 11

value: Littermate Pkd1 Het Cre BL 3


title: Donor #1

description:
S4, 2 x 150 bp, lane (2000-2500  M read pairs)
DG-21_Donor_1


title: Donor #2

description:
S4, 2 x 150 bp, lane (2000-2500  M read pairs)
DG-22_Donor_2


title: Normal Chow Diet 9

value: Littermate Pkd1 Homo Cre BL 3


title: Patient #24

description:
S4, 2 x 150 bp, lane (2000-2500  M read pairs)
DG-20_Patient_24

source_name: adolescent undergoing fertility preservation

value: adolescent


title: Patient #22

description:
S4, 2 x 150 bp, lane (2000-2500  M read pairs)
DG-18_Patient_22


title: Normal Chow Diet 5

value: Littermate Pkd1 Het Cre BL 1


title: Patient #17

description:
S4, 2 x 150 bp, lane (2000-2500  M read pairs)
DG-15_Patient_17


title: Patient #18

description:
S4, 2 x 150 bp, lane (2000-2500  M read pairs)
DG-16_Patient_18


title: Patient #23

description:
S4, 2 x 150 bp, lane (2000-2500  M read pairs)
DG-19_Patient_23


title: Normal Chow Diet 3

value: Littermate Pkd1 Homo Cre BL 2


title: Patient #16

description:
S4, 2 x 150 bp, lane (2000-2500  M read pairs)
DG-14_Patient_16


title: Patient #20

description:
S4, 2 x 150 bp, lane (2000-2500  M read pairs)
DG-17_Patient_20


title: Normal Chow Diet 2

value: Littermate Pkd1 Homo Cre BL 1


title: Patient #14

description:
S4, 2 x 150 bp, lane (2000-2500  M read pairs)
DG-13_Patient_14

value: Primary Cells


title: Patient #11

description:
S4, 2 x 150 bp, lane (2000-2500  M read pairs)
DG-10_Patient_11

value: Human primary cumulus cells


title: Patient #13

description:
S4, 2 x 150 bp, lane (2000-2500  M read pairs)
DG-12_Patient_13


title: Patient #10

description:
S4, 2 x 150 bp, lane (2000-2500  M read pairs)
DG-9_Patient_10


title: Patient #12

description:
S4, 2 x 150 bp, lane (2000-2500  M read pairs)
DG-11_Patient_12


title: Hepatocyte organoids, RGF, Day 6, 3

city: Boston

first: Yuchen

last: Liu

state: Massachusetts

address: 188 Longwood Avenue, REB 514B

institute: Harvard school of dental medicine

data_processing:
Sequence alignment were performed using STAR aligner.
Paired reads were then counted using ‘featureCounts’ in The Subread software
Raw counts were normalized using the edgeR package
Assembly: mm10
Supplementary files format and content: tab delimited text file include normalized CPM values for each sample

growth_protocol: The HOs were maintained in the original HO growth medium with growth factors (GFs) (+GF medium). The +GF medium for  HO culture contains Advanced DMEM/F12 with B27 minus vitamin A, 10mM HEPES, GlutaMAX™, and Penicillin-Streptomycin (Thermo Fisher Scientific), 15% RSPO1 conditioned medium (home-made), 3μm CHIR99021 (MCE), 50ng/ml EGF (Biolegend), 25ng/ml HGF (Biolegend), 50ng/ml FGF7 (Peprotech), 50ng/ml FGF10 (Biolegend), 1μM A83-01 (Sigma), 5μM Rho Inhibitor γ-27632 (MCE), 10nM gastrin (Sigma), 10 mM Nicotinamide (Sigma), and 1mM N-acetylcysteine (Sigma).

extract_protocol:
Organoids were retrieved from BME using Cultrex Organoid Harvesting Solution and pelleted by centrifuge at 50g for 3 minutes. RNA was isolated from the organoid pellet using PureLinkTM RNA mini kit (Thermo fisher scientific) according to the manufacturer's instruction.
DNA was removed from RNA using RapidOut DNA Removal Kit (Thermo Fisher Scientific) according to the manufacturer's instruction. After measuring RNA quantity and quality by Agilent 2200 TapeStation, 400ng-1000ng RNA per sample reaction were used for mRNA isolation using NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). Libraries were prepared using xGen™ RNA Library Prep Kit (IDT) according to the manufacturer's instruction.

treatment_protocol: The HOs were switched to the maturation medium for HO maturation. The basal medium for human and mouse HO maturation is Growth factors removed (RGF) medium, which includes William's E Medium with B27 minus vitamin A, 10mM HEPES, GlutaMAXTM and Penicillin-Streptomycin (Thermo Fischer Scientific), 50μg/ml Primocin (InvivoGen), 15% RSPO1 conditioned medium (house-made), 3μM CHIR99021 (MCE), 1μM A83-01 (MCE), 5μM Rho Inhibitor γ-27632 (MCE), 10nM gastrin (Sigma), 2.5 mM Nicotinamide (Sigma), and 1.25 mM N-acetylcysteine (Sigma). Additional components were added to RGF medium for hepatic maturation of HOs. For maturation of mouse HOs, these medium incude: RGF +T3: 10nM Triiodothyronine(T3) in RGF medium; RGF +DEX: 200nM dexamethasone (DEX) in RGF medium; RGF +T3 +DEX: 10nM T3 and 200nM DEX in RGF medium. For HO dedifferentiation, the HOs were cultured in the RGF +T3 condition for 6 days, and switched to +GF condition for another 6 days. To overexpress CTNNB1ΔN90 in the HOs, AAV-TBG-CTNNB1ΔN90 was mixed with fragmented HOs in BME at a concentration of 2x10^10 GC/ml during passage.

value: Hepatocyte organoids

value: hepatocytes

value: wild type

value: RGF, Day6

tag: time


title: Hepatocyte organoids, RGF, Day 6, 2

value: liver


title: Patient #8

description:
S4, 2 x 150 bp, lane (2000-2500  M read pairs)
DG-8_Patient_8


title: Hepatocyte organoids, RGF, Day 3, 3

value: RGF, Day3


title: Patient #7

description:
S4, 2 x 150 bp, lane (2000-2500  M read pairs)
DG-7_Patient_7


title: Hepatocyte organoids, RGF, Day 3, 2


title: Normal Chow Diet 6

value: Littermate Pkd1 Het Cre BL 2


title: Patient #6

description:
S4, 2 x 150 bp, lane (2000-2500  M read pairs)
DG-6_Patient_6


title: USA100 loratadine cotreated biol rep C

city: High Point

first: Heather

middle: Bennett

last: Miller

state: NC

address: One University Parkway

department: Chemistry

institute: High Point University

data_processing:
Quality control of resulting reads included removing adapter-containing reads, removing reads where “N” was > 10%, and removing low-quality reads where the quality value of over 50% of the bases was ≤ 5.
The remaining reads were mapped to the reference genome (Staphylococcus aureus subsp. aureus N315, NC_002745.2) using Bowtie2.
Gene expression levels were quantified as fragments per kilobase of transcript sequence per million base pairs sequenced (FPKM) and averaged among biological triplicate samples.
Pearson correlation analysis quantified the correlation among biological triplicates.
Assembly: Staphylococcus aureus subsp. aureus N315, NC_002745.2
Supplementary files format and content: An Excel spreadsheet for all treatment comparison groups that contain all analyzed replicates, gene information, read counts, fpkm, log2fold change and adjusted pvalues

organism: Staphylococcus aureus

source_name: bacterial cells

growth_protocol: S. aureus USA100 (BAA-1753) was purchased from American Type Culture Collection.  Cultures were grown overnight in CAMHB at 37 °C with shaking. Mid-log-phase cultures were diluted to 5 × 105CFU mL–1in CAMHB.

extract_protocol:
Total RNA was purified from 3mL of culture using a Qiagen RNeasy kit and Thermo's Turbo DNase kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The cell suspension (3 mL) was aliquoted into sterile culture tubes, and loratadine was added to the appropriate concentration (≤25% of the compound MIC = 50 uM). Compound 8 was added to a separate culture tube to the appropriate concentration  (≤25% of the compound MIC = 25 uM). Oxacillin was added to a separate culture tube at 4 ug/mL. Cotreatment consisted of both oxacillin (4 ug/mL) and loratadine (50uM) or oxacillin (4 ug/mL) and compound 8 (25uM). Untreated cultures served as negative controls. These treatments continued for 1 hour while in the shaking incubator.

value: bacterial cells

value: cotreated with loratadine and oxacillin


title: Patient #4

description:
S4, 2 x 150 bp, lane (2000-2500  M read pairs)
DG-4_Patient_4


title: Hepatocyte organoids, RGF, Day 3, 1


title: Patient #2

description:
S4, 2 x 150 bp, lane (2000-2500  M read pairs)
DG-2_Patient_2


title: Patient #3

description:
S4, 2 x 150 bp, lane (2000-2500  M read pairs)
DG-3_Patient_3


title: USA100 compound 8 treated biol rep C

value: compound 8 treated, 25 uM


title: USA100 compound 8 cotreated biol rep C

value: cotreated with compound 8 and oxacillin


title: USA100 oxacillin treated biol rep C

value: oxacillin treated, 4 ug/mL


title: USA100 loratadine treated biol rep C

value: loratadine treated, 50 uM


title: Patient #1

description:
S4, 2 x 150 bp, lane (2000-2500  M read pairs)
DG-1_Patient_1

value: adolescent


title: H460 cells, kras mutLKB1 WT rep2

city: CHICAGO

first: Constantinos

last: chronis

address: 900 S Ashland Ave, Mbrb 2370

department: Biochemistry and Molecular Genetics

institute: UIC

description:
WT_Neg_HG1_2_3_ATAC_peaks.narrowPeak
WT_Neg_HG1_2_3_ATAC_sorted_dedup.bam_rpkm.bw

data_processing:
Basecalls performed using CASAVA version 1.4
ATAC reads were aligned to the  GRCh38 genome assembly using Bowtie2 aligner only those reads that aligned to a unique position with no more than two sequence mismatches were retained for further analysis
peaks were called using MACS2 software
RPKM normalised bigwig files were generated using the bamCoverage command from bedtools (bamCoverage -of bigwig --normalizeUsing=RPKM -v -b)
Assembly: GRCh38
Supplementary files format and content: bigwig files obtained post mapping to GRCh38 normalised by RPKM method

extract_protocol:
100000 cells (H460) were were re-suspended in 50μl lysis buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, and 1 × Complete Protease inhibitor (Roche)) and spun at 500g for 10 min at 4 °C to collect nuclei. Nuclei were washed in 1x PBS and subsequently re-suspended in 50 μl Transposase reaction (25 μl 2 × Tagmentation buffer, 22.5 μl water, 2.5 μl Tn5 Transposase enzyme, following instructions by Illumina). Reactions were incubated for 30 min at 37 °C and DNA purified using Qiagen MinElute columns (Qiagen). The transposed DNA was subsequently amplified with custom primers as described (Buenrostro et al., 2013) for 7-9 cycles and libraries were visualized on a 2% TBE gel prior to sequencing with a single-end-sequencing length of 50 nucleotides.
NovaSeqSP
PE150 bp

value: NSCLC-large cell carcinoma-derived cell line

value: kras mutLKB1 WT


title: USA100 untreated biol rep C

value: untreated


title: USA100 loratadine cotreated biol rep B


title: USA100 compound 8 cotreated biol rep B


title: Hepatocyte organoids, RGF, Day 6, 1

value: Hepatocyte organoids


title: H460 cells, Kras mut; LKB1 loss rep3

description:
EV_Neg_HG1_2_3_ATAC_peaks.narrowPeak
EV_Neg_HG1_2_3_ATAC_sorted_dedup.bam_rpkm.bw

value: Kras mut; LKB1 loss


title: USA100 compound 8 treated biol rep B


title: H460 cells, kras mutLKB1 WT rep3


title: H460 cells, Kras mut; LKB1 loss rep2


title: H460 cells, kras mutLKB1 WT rep1


title: USA100 loratadine treated biol rep B


title: Vessel Organoids 3

city: Cincinnati

first: Ziyuan

last: Guo

address: 3333 Burnet Ave

institute: CCHMC

data_processing:
Raw reads in fastq format were trimmed to remove the adaptor sequence and the reads with adaptor contaminants and low-quality reads using TrimGalore (v 0.6.6)
Preprocessed reads were then aligned to the human genome (build GRCh38) using STAR (v2.7.9) with the default settings
Gene counts were obtained using FeatureCounts (v2.0.3)
Differential expression gene (DEGs) analysis was conducted using the R statistical package DESeq2 with an FDR of 0.05 and a fold change threshold of log2 (fold change) > ±1
Assembly: GRCh38
Supplementary files format and content: tab-delimited txt file includes raw counts for each Sample

source_name: iPS

growth_protocol: iPSCs were expanded onto fresh vitronectin-coated plate with Essential 8 medium, passaged with ReleSRTM every 3-4 days

extract_protocol:
Total cellular RNA was isolated using the Invitrogen mirVana kit in accordance with the manufacturer’s instructions
Libraries were generated from 1 μg of total RNA using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB), as per the manufacturer’s protocol.

treatment_protocol: iPSCs were differentiated into cerebral organoids, and vessel organoids. Cerebral organoid and vessel organoid were fused to get BBB assemblods

value: iPS

value: iPS derived vessel organoids 3

value: WT

value: iPS differentiation


title: USA100 untreated biol rep B


title: H460 cells, Kras mut; LKB1 loss rep1


title: Vessel Organoids 2

value: iPS derived vessel organoids 2


title: HiFi_brain_organoid

city: San Diego

first: Sheng

last: Zhong

state: California

address: 9500 Gilman Dr, La Jolla

department: Shu Chien-Gene Lay Department of Bioengineering

institute: UC San Diego

description: Fresh Frozen 20 micron sections

data_processing:
Spatial barcodes are deduplicated and indexed using bwa index
Raw HiFi read pairs are preprocessed using PEAR and FASTP to remove overlapping ends, polyG and polyX tails, too short reads
HiFi RNA ends (R2) are aligned to reference genome using STAR and uniquely mapped reads are extracted
HiFi spatial ends (R1) are aligned to spatial barcodes using BWA MEM
HiFi spatial ends aligned with highest score are extracted and spatial location is decoded
Spatial coordinates and gene expression information are integrated
ROI is selected by tile IDs. List of spot IDs, gene IDs and spot by gene expression matrix are extracted for ROI
Assembly: hg38
Supplementary files format and content: hifi_gene_by_spot_Tile1203.mtx: spot by gene expression matrix
Supplementary files format and content: hifi_gene_by_spot_Tile1203.spot: list of spot IDs
Supplementary files format and content: hifi_gene_by_spot_Tile1203.gene.ensemblID: list of gene IDs
Library strategy: spatial transcriptomics

source_name: H9 ESCs derived cerebral orgnoid assembloid with blood vessels organoid

growth_protocol: Astrocytic promoted cerebral organoids and blood vessel organoids were cultured seprarately and then embedded together with matrigel matrix.

extract_protocol:
HIFI-slides spatial protocol V1 and V2, DOI: dx.doi.org/10.17504/protocols.io.3byl4by18vo5/v1
Tissue permeabilization with RNA capture. cDNA synthesis and the Klenow + Random sequence second strand extraction. Amplification with PCR, coloumn purification and gel-based size selection.

treatment_protocol: Fresh Frozen, sectioned to 20 to 30um

value: Control


title: USA100 loratadine cotreated biol rep A

value: bacterial cells

value: cotreated with loratadine and oxacillin


title: USA100 compound 8 cotreated biol rep A

value: cotreated with compound 8 and oxacillin


title: Vessel Organoids 1

value: iPS derived vessel organoids 1


title: Cerebral Organoids 3

value: iPS derived cerebral organoids 3


title: USA100 loratadine treated biol rep A

value: loratadine treated, 50 uM


title: Cerebral Organoids 2

value: iPS derived cerebral organoids 2


title: USA100 compound 8 treated biol rep A

value: compound 8 treated, 25 uM


title: Cerebral Organoids 1

value: iPS derived cerebral organoids 1


title: BBB Assembloids, GFP positive 3

value: iPS derived BBB assembloids 3

value: organoid differentiation and fusion


title: USA100 untreated biol rep A

value: untreated


title: USA100 oxacillin treated biol rep A

value: oxacillin treated, 4 ug/mL


title: BBB Assembloids, GFP positive 2

value: iPS

value: iPS derived BBB assembloids 2

value: WT


title: BBB Assembloids, GFP positive 1

value: iPS derived BBB assembloids 1


title: BBB Assembloids, GFP negative 2


title: USA100 oxacillin treated biol rep B

value: bacterial cells


title: BBB Assembloids, GFP negative 3


title: BBB Assembloids, GFP negative 1


title: NASH_rep3 [22093D1]

city: Changsha

first: xiaohua

last: luo

state: hunan

address: 139 Renmin Road

institute: The Second Xiangya Hospital of Central South University

data_processing:
Skewer was used to process the raw data and FastQC v0.11.2 was utilized to verify the quality of the data. STAR (version 2.5.3a) was employed to align the clean reads to the Human genome hg38. StringTie software (version 1.3.1c) was utilized to count the raw sequence counts of established genes in all samples.
Assembly: Human genome hg38
Supplementary files format and content: Count table

source_name: Liver

extract_protocol:
The RNAmini kit (Qiagen, Germany) was used to extract total RNA from every liver tissue sample.
The TruSeq RNA sample preparation kit (Illumina, San Diego, CA, USA) was used to construct strand-specific libraries.

tag: disease state

value: non-alcoholic steatohepatitis (NASH)

value: Liver

value: Liver cell


title: KBc

city: Lausanne

first: Ludovic

last: Telley

address: Department of Biomedical Sciences University of Lausanne Rue du Bugnon 9

country: Switzerland

institute: UNIL

description: Tom-

library_source: transcriptomic single cell

data_processing:
Alignment of sequenced reads to the mouse genome (GRCm38) and filtered gene–barcode matrices were realized by running Cell Ranger Single-Cell Software Suite v5.0.1 (10X Genomics).
Assembly: GRCm38
Supplementary files format and content: singlecell_countmatrix.tsv.gz: is a count matrix in tab-separated format. It contains the result of the single cell quantification for all genes. The  values represent the number of exonic reads mapping into each gene after UMI correction. The first columns contain the gene name that is quantified.
Supplementary files format and content: singlecell_metadata.tsv: is a table containing metadata information for each cells analyse in the paper in tab-separated.
Supplementary files format and content: processed_script.gz : is a compressed file containing the R script and the RDS files to load

source_name: Brain cells

extract_protocol:
Protocol adapted from (Mattei et al., 2020). In brief, mice were anesthetized by i.p. injection of pentobarbital (150 mg/kg) and intracardially perfused with 30 ml cold PBS (pH 7.3-7.4). The brain was collected and finely chopped with a few drops of Hibernate A (Hibernate®A without phenol red, BrainBits) before complete dissociation in 1.5 ml Hibernate A in a 1 ml douncer (loose pestle). The cell suspension was filtered twice in a prewet 70 mm cell strainer (#15370801, Fisher Scientific), the rubber tip of a 1 ml syringe was used to facilitate the filtering. The cell suspension was transferred to a precooled 15 ml tube and centrifuged at 500 x g for 6 min. The supernatant was aspired, and the cell pellet was resuspended in 2 ml cold PBS (pH 7.3-7.4), before adding 1 ml isotonic percoll in PBS (pH 7.3-7.4) (#GE17-0891-01, Sigma-Aldrich). The suspension was mixed well before 4 ml cold PBS (pH 7.3-7.4) was gently added on top of the cell suspension. The layered sample was centrifuged at 3000 x g, 10 min. The supernatant and the myelin disk were gently aspired. The cell pellet was gently washed by adding 4 ml cold PBS (pH 7.3-7.4) and gently tilting the tube back and forth before centrifuging at 450 rcf, 10 min. Cell pellets used for FACS were dissolved in 500 ul EDTA-DPBS (#E8008, Merck Millipore), cell pellets used for scRNA sequencing were dissolved in 500 ml PBS (pH 7.3-7.4).
After sorting, cells were immediately processed according to the 10X Chromium protocol. Briefly, an appropriate volume of each cell suspension containing cells from tdTomato positive and tdTomato negative conditions were combined with 10X Chromium reagent mix and samples were loaded into two separate lanes. Cell capture, lysis, mRNA reverse transcription, cDNA amplification and libraries were performed following 10X Genomics Chromium dual indexing Single Cell 3' V3.1 reagent kit instructions. Libraries were then multiplexed and sequenced according manufacture recommendations with paired-end reads using a HiSeq4000 platform (Illumina) with an expected depth of 100’000 reads per single cells. All the sequencing experiments were performed within the Genomics Core Facility of the University of Lausanne.

value: Brain cells

value: Tom-


title: NASH_rep4 [22095D1]


title: GFP-LC3 oHSC_LO_144

city: New York

first: Paul

middle: Vincent

last: Dellorusso

state: NY

address: 701 West 168th Street, 724 Hammer Health Sciences Center

department: Genetics and Development

institute: Columbia University Irving Medical Center

description:
smartseq2
fcounts2.txt

data_processing:
scRNA-Seq reads were aligned to the mouse genome (mm10) with the STAR aligner (version 2.7.3a), sequences of eGFP and rat Map1lc3b were included in the index file, and subread featureCounts (version 2.0.0) function using the ENSEMBL v93 annotation.
Cells with >120,000 nuclear mapped reads, fraction of nuclear mapped reads mapped to genes >15% and fraction of mitochondrial reads relative to reads mapped to genes <20% were retained for downstream analysis.
Counts were normalised using size factor methods from DESeq2 and ERCCs were used to determine technical noise and highly variable genes.
Assembly: mouse
Supplementary files format and content: txt files containing raw fcount matrices

source_name: bone marrow

extract_protocol:
BM derived cells were isolated , crushed and filtered through 40µm nylon mesh. These cells were stained for surface markers and sorted . Single cells were individually sorted by fluorescence-activated cell sorting into 96-well PCR plates containing lysis buffer (10% Triton X-100, SUPERase-In RNase Inhibitor 20U/μl (Thermo Fisher Scientific) and DEPC-treated or Rnase-free H20), at 4°C.
Individual scRNA-seq libraries were prepared using a modified smartseq2 protocol (PMID: 30050112, PMID: 24385147 and PMID: 34057731).

value: bone marrow

tag: age

value: old

value: Haematopoietic stem cell

value: steady state isolation


title: NASH_rep2 [22092D1]


title: GFP-LC3 oHSC_HI_135

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_MID_144

description:
smartseq2
fcounts2.txt


title: KAc

description: Tom+

value: Tom+


title: GFP-LC3 oHSC_MID_143

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_LO_1413

description:
smartseq2
fcounts2.txt


title: GFP-LC3 yHSC_138

description:
smartseq2
fcounts2.txt

value: young


title: NAFL_rep5 [22123D1]

value: non-alcoholic fatty liver disease (NAFLD)

value: untreated


title: NAFL_rep6 [22130D1]


title: GFP-LC3 oHSC_HI_134

description:
smartseq2
fcounts2.txt


title: NASH_rep1 [22054D1]


title: NAFL_rep4 [22120D1]


title: GFP-LC3 oHSC_LO_142

description:
smartseq2
fcounts2.txt


title: GFP-LC3 yHSC_137

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_HI_136

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_MID_142

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_HI_133

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_MID_141

description:
smartseq2
fcounts2.txt


title: NAFL_rep2 [21151D1]


title: GFP-LC3 yHSC_139

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_LO_141

description:
smartseq2
fcounts2.txt


title: Control_rep5 [22113D1]

value: healthy control


title: Control_rep4 [22085D1]


title: GFP-LC3 yHSC_136

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_HI_132

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_MID_140

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_LO_140

description:
smartseq2
fcounts2.txt


title: NAFL_rep3 [22105D1]


title: H128-DN5-Input

city: Guangzhou

first: Hong

last: Wang

address: 132, Waihuandonglu, Daxue Cheng

department: School Of Pharmaceutical Sciences

institute: Sun Yat-sen University

data_processing:
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01.bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

source_name: Homo sapiens

growth_protocol: SCLC cells were maintained in RPMI1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
sample 4-7:Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
sample 4-7:ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

treatment_protocol: H128 cells were treated with DN200434 for 48 h or transfected with ERRG siRNA or vehicle siRNA for 48 h.

value: Homo sapiens

value: tumor cells


title: H128-DN5-H3K27ac, ChIP


title: H128-0-H3K27ac, ChIP


title: GFP-LC3 oHSC_MID_139

description:
smartseq2
fcounts2.txt


title: GFP-LC3 yHSC_135

description:
smartseq2
fcounts2.txt


title: H128-0-Input


title: GFP-LC3 oHSC_LO_139

description:
smartseq2
fcounts2.txt


title: NAFL_rep1 [21149D1]


title: Control_rep6 [22114D1]


title: GFP-LC3 oHSC_HI_130

description:
smartseq2
fcounts2.txt


title: PBMC, Control, rep 10

city: Rome

first: Luisa

last: Lo Iacono

address: via del fosso di Fiorano 64

department: behavioral neuroscience

institute: Fondazione Santa Lucia IRCCS

data_processing:
Illumina novaSeq base call (BCL) files were converted in fastq file through bcl2fastq(version v2.20.0.422)
Sequence reads were trimmed using trimmomatic-0.39  to remove adapter sequences, poly-A tails and low-quality end bases (regions with average quality below 30)
Alignment was performed with Hisat2- 2.2.1  on GRCh38 assembly
The expression levels of genes were determined withR package  Rsubread by using Ensembl genes annotations.
Individual sample counts were normalized via Relative Log Expression (RLE) using DESeq2 R library
Assembly: GRCh38 genome from UCSC genome browser
Supplementary files format and content: rawcounts.txt : include raw gene counts values for each sample in a matrix.
Supplementary files format and content: norm_count.txt: includes normalized gene counts values for each sample in a matrix (after DeSeq normalization)

source_name: peripheral blood mononuclear cells

extract_protocol:
PBMCs were isolated by density gradient over Ficoll-Hypaque (GE Healthcare BioSciences) and RNA was purified using Total RNA purification Kit (Norgen Biotek). RNA quantity was determined using a NanoDrop UV–VIS spectrophotometer  and quality checked via bioanalyzer assay
Libraries were prepared from 100ng of total RNA using the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen GmbH). Libraries were sequenced on a NovaSeq 6000 sequencing system using an S1, 100 cycles flow cell (Illumina Inc.)

value: peripheral blood mononuclear cells

tag: child experience

value: no trauma


title: PBMC, Control, rep 9


title: PBMC, Control, rep 8


title: GFP-LC3 oHSC_MID_138

description:
smartseq2
fcounts2.txt


title: GFP-LC3 yHSC_134

description:
smartseq2
fcounts2.txt


title: PBMC, Control, rep 7


title: PBMC, Control, rep 6


title: GFP-LC3 oHSC_LO_138

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_HI_129

description:
smartseq2
fcounts2.txt


title: PBMC, Control, rep 5


title: GFP-LC3 yHSC_133

description:
smartseq2
fcounts2.txt


title: Control_rep3 [22068D1]

value: Liver


title: Control_rep2 [21124D1]

value: Liver cell


title: Control_rep1 [21120D1]


title: PBMC, Control, rep 4


title: GFP-LC3 oHSC_MID_137

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_LO_137

description:
smartseq2
fcounts2.txt


title: PBMC, Control, rep 3


title: GFP-LC3 oHSC_HI_131

description:
smartseq2
fcounts2.txt


title: GFP-LC3 yHSC_132

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_HI_128

description:
smartseq2
fcounts2.txt


title: PBMC, Abuse + neglect, rep 10

value: abuse + neglect


title: PBMC, Control, rep 2


title: GFP-LC3 oHSC_MID_136

description:
smartseq2
fcounts2.txt


title: GFP-LC3 yHSC_131

description:
smartseq2
fcounts2.txt


title: PBMC, Abuse + neglect, rep 7


title: PBMC, Abuse + neglect, rep 8


title: GFP-LC3 oHSC_LO_135

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_MID_135

description:
smartseq2
fcounts2.txt


title: PBMC, Abuse + neglect, rep 5


title: PBMC, Abuse + neglect, rep 4


title: PBMC, Abuse + neglect, rep 2


title: PBMC, Abuse + neglect, rep 3


title: PBMC, Abuse + neglect, rep 1


title: GFP-LC3 oHSC_MID_134

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_LO_134

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_HI_127

description:
smartseq2
fcounts2.txt


title: GFP-LC3 yHSC_129

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_HI_126

description:
smartseq2
fcounts2.txt


title: PBMC, Control, rep 1


title: PBMC, neglect, rep 6

value: neglect


title: PBMC, neglect, rep 5


title: GFP-LC3 oHSC_LO_133

description:
smartseq2
fcounts2.txt

value: bone marrow


title: PBMC, Abuse + neglect, rep 9


title: PBMC, neglect, rep 4


title: PBMC, neglect, rep 8


title: PBMC, Abuse + neglect, rep 6


title: GFP-LC3 oHSC_MID_132

description:
smartseq2
fcounts2.txt

value: old


title: GFP-LC3 oHSC_LO_132

description:
smartseq2
fcounts2.txt

value: Haematopoietic stem cell


title: PBMC, neglect, rep 3


title: GFP-LC3 yHSC_128

description:
smartseq2
fcounts2.txt

value: steady state isolation


title: GFP-LC3 yHSC_127

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_HI_125

description:
smartseq2
fcounts2.txt


title: GFP-LC3 yHSC_130

description:
smartseq2
fcounts2.txt


title: PBMC, neglect, rep 2


title: PBMC, neglect, rep 1


title: PBMC, abuse, rep 6

value: abuse


title: GFP-LC3 oHSC_MID_131

description:
smartseq2
fcounts2.txt


title: PBMC, abuse, rep 8


title: PBMC, neglect, rep 7


title: GFP-LC3 oHSC_HI_124

description:
smartseq2
fcounts2.txt


title: PBMC, abuse, rep 7


title: GFP-LC3 oHSC_LO_131

description:
smartseq2
fcounts2.txt


title: GFP-LC3 yHSC_126

description:
smartseq2
fcounts2.txt

value: young


title: GFP-LC3 oHSC_MID_133

description:
smartseq2
fcounts2.txt


title: PBMC, abuse, rep 4


title: PBMC, abuse, rep 5


title: GFP-LC3 oHSC_MID_130

description:
smartseq2
fcounts2.txt


title: GFP-LC3 yHSC_125

description:
smartseq2
fcounts2.txt


title: PBMC, abuse, rep 3


title: PBMC, abuse, rep 2


title: GFP-LC3 oHSC_MID_129

description:
smartseq2
fcounts2.txt


title: PBMC, abuse, rep 9


title: PBMC, abuse, rep 1


title: s92_PFC_RNA

city: Munich

first: Elisabeth

last: Binder

address: Kraepelinstr. 2-10

country: Germany

institute: Max Planck Institute of Psychiatry

description:
Single-cell RNA sequencing  (10xGenomics)
adata_RNA.h5ad.gz

data_processing:
Sequence reads were demultiplexed using the sample index, aligned to a pre-mRNA reference (GRCh38_ensrel98) and UMI were counted after demultiplexing of nuclei barcodes using Cell Ranger v6.0.1.
Downsampling of reads per cell to 75% quantile (14,786 reads per cell) with DropletUtils v1.12.2.
Quality control of count matrix with Scanpy v1.7.1 (filtered out nuclei with counts < 500, genes < 300, Mito % ≥ 15 and genes expressed in < 500 nuclei, 1 sample with overall low data quality).
Removal of doublets with DoubletDetection v3.0. Normalization and log-transformation with sctransform v0.3.2.
Highly variable genes were identified and dimensionality reduction, including principal component analysis (PCA) and uniform manifold approximation and projection (UMAP) was performed with Scanpy.
Nuclei were clustered based on highly variable genes using the leiden clusterin algorithm (resolution 1.0).
Four donors were filtered out due to the fact that more than 50% of their nuclei were located within one cluster, resulting in 787,046 nuclei from 87 donors.
Assembly: GRCh38
Supplementary files format and content: h5ad file with processed snRNA-seq data (including cell type annotations) in anndata format

molecule: nuclear RNA

source_name: brain

extract_protocol:
Nuclei were isolated from frozen, dissected brain samples (OFC, BA11; 50 - 60 mg) by dounce-homogenisation in nuclei extraction buffer. Homogenate was layered onto a sucrose cushion and ultra-centrifuged. Nuclei pellet was resuspended in resuspension buffer, filtered through a cell strainer cap, stained with DAPI and counted using a hemocytometer.
Single nuclei RNA-seq libraries were prepared following the user guide of 10X Genomics (Chromium Single Cell 3’ Reagents kit v3.1) with a target recovery of 10,000 nuclei per sample.
Libraries were assessed using a High Sensitivity DNA Analysis Kit for the 2100 Bioanalyzer (Agilent), were then pooled equimolarily and treated with Illumina Free Adapter Blocking Reagent before sequencing on the NovaSeq 6000 System (Illumina).

value: brain

tag: disease status

value: Cases

tag: classification

value: Schizophrenia

tag: Sex

value: Female

tag: ethnicity

value: European

tag: ph

tag: pmi

tag: rin

tag: lib batch


title: GFP-LC3 oHSC_LO_129

description:
smartseq2
fcounts2.txt

tag: tissue


title: s91_PFC_RNA

value: Controls

value: Control

value: Male


title: GFP-LC3 oHSC_LO_130

description:
smartseq2
fcounts2.txt

tag: cell type


title: GFP-LC3 oHSC_LO_136

description:
smartseq2
fcounts2.txt

tag: genotype


title: GFP-LC3 yHSC_124

description:
smartseq2
fcounts2.txt

tag: treatment


title: s90_PFC_RNA


title: GFP-LC3 oHSC_MID_128

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_HI_123

description:
smartseq2
fcounts2.txt


title: s89_PFC_RNA


title: GFP-LC3 oHSC_LO_128

description:
smartseq2
fcounts2.txt


title: s87_PFC_RNA


title: s88_PFC_RNA

value: MajorDepression


title: GFP-LC3 oHSC_HI_122

description:
smartseq2
fcounts2.txt


title: s86_PFC_RNA


title: s83_PFC_RNA


title: s84_PFC_RNA


title: GFP-LC3 yHSC_123

description:
smartseq2
fcounts2.txt


title: s85_PFC_RNA


title: GFP-LC3 oHSC_MID_127

description:
smartseq2
fcounts2.txt


title: GFP-LC3 yHSC_122

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_MID_126

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_LO_125

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_MID_125

description:
smartseq2
fcounts2.txt


title: s82_PFC_RNA


title: GFP-LC3 yHSC_121

description:
smartseq2
fcounts2.txt


title: s77_PFC_RNA

value: BipolarDisorder


title: s80_PFC_RNA


title: s81_PFC_RNA


title: GFP-LC3 oHSC_HI_120

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_HI_121

description:
smartseq2
fcounts2.txt


title: s79_PFC_RNA

value: SchizoaffectiveDisorder


title: GFP-LC3 oHSC_MID_124

description:
smartseq2
fcounts2.txt

value: bone marrow


title: s78_PFC_RNA


title: s76_PFC_RNA


title: s74_PFC_RNA


title: GFP-LC3 oHSC_LO_124

description:
smartseq2
fcounts2.txt

value: old


title: GFP-LC3 yHSC_119

description:
smartseq2
fcounts2.txt

value: Haematopoietic stem cell


title: s73_PFC_RNA


title: GFP-LC3 oHSC_MID_123

description:
smartseq2
fcounts2.txt

value: steady state isolation


title: GFP-LC3 oHSC_LO_127

description:
smartseq2
fcounts2.txt


title: s72_PFC_RNA


title: GFP-LC3 oHSC_LO_123

description:
smartseq2
fcounts2.txt


title: s75_PFC_RNA


title: s69_PFC_RNA


title: GFP-LC3 oHSC_LO_126

description:
smartseq2
fcounts2.txt


title: GFP-LC3 yHSC_118

description:
smartseq2
fcounts2.txt


title: s71_PFC_RNA


title: s70_PFC_RNA


title: GFP-LC3 oHSC_HI_119

description:
smartseq2
fcounts2.txt


title: GFP-LC3 yHSC_120

description:
smartseq2
fcounts2.txt


title: s68_PFC_RNA


title: s67_PFC_RNA


title: GFP-LC3 oHSC_MID_122

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_HI_118

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_LO_122

description:
smartseq2
fcounts2.txt


title: s66_PFC_RNA


title: s65_PFC_RNA


title: GFP-LC3 oHSC_MID_121

description:
smartseq2
fcounts2.txt


title: GFP-LC3 yHSC_117

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_LO_120

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_LO_121

description:
smartseq2
fcounts2.txt


title: s64_PFC_RNA


title: GFP-LC3 oHSC_MID_120

description:
smartseq2
fcounts2.txt


title: s61_PFC_RNA


title: s58_PFC_RNA


title: GFP-LC3 oHSC_HI_117

description:
smartseq2
fcounts2.txt


title: s62_PFC_RNA


title: s63_PFC_RNA


title: s57_PFC_RNA


title: s60_PFC_RNA


title: GFP-LC3 yHSC_116

description:
smartseq2
fcounts2.txt


title: s56_PFC_RNA


title: s59_PFC_RNA


title: GFP-LC3 yHSC_115

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_LO_119

description:
smartseq2
fcounts2.txt


title: s55_PFC_RNA


title: GFP-LC3 oHSC_MID_118

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_LO_118

description:
smartseq2
fcounts2.txt


title: GFP-LC3 yHSC_114

description:
smartseq2
fcounts2.txt


title: s51_PFC_RNA


title: s54_PFC_RNA


title: s50_PFC_RNA


title: GFP-LC3 oHSC_LO_117

description:
smartseq2
fcounts2.txt


title: s53_PFC_RNA


title: s49_PFC_RNA


title: s48_PFC_RNA


title: GFP-LC3 yHSC_113

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_HI_115

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_MID_117

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_MID_119

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_MID_116

description:
smartseq2
fcounts2.txt


title: s45_PFC_RNA


title: GFP-LC3 yHSC_112

description:
smartseq2
fcounts2.txt


title: s46_PFC_RNA


title: GFP-LC3 oHSC_HI_114

description:
smartseq2
fcounts2.txt


title: s44_PFC_RNA


title: GFP-LC3 oHSC_HI_116

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_MID_115

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_LO_115

description:
smartseq2
fcounts2.txt


title: s47_PFC_RNA


title: s43_PFC_RNA


title: GFP-LC3 yHSC_111

description:
smartseq2
fcounts2.txt


title: s42_PFC_RNA


title: s40_PFC_RNA


title: s52_PFC_RNA


title: s41_PFC_RNA


title: GFP-LC3 oHSC_HI_113

description:
smartseq2
fcounts2.txt


title: s38_PFC_RNA


title: s36_PFC_RNA


title: GFP-LC3 yHSC_110

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_HI_112

description:
smartseq2
fcounts2.txt


title: s34_PFC_RNA


title: GFP-LC3 oHSC_LO_113

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_MID_113

description:
smartseq2
fcounts2.txt


title: s35_PFC_RNA


title: s33_PFC_RNA


title: s32_PFC_RNA


title: GFP-LC3 yHSC_109

description:
smartseq2
fcounts2.txt


title: s30_PFC_RNA


title: s29_PFC_RNA


title: s28_PFC_RNA


title: GFP-LC3 oHSC_LO_112

description:
smartseq2
fcounts2.txt


title: GFP-LC3 yHSC_108

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_HI_110

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_MID_111

description:
smartseq2
fcounts2.txt


title: s27_PFC_RNA


title: s39_PFC_RNA


title: GFP-LC3 oHSC_MID_114

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_LO_114

description:
smartseq2
fcounts2.txt


title: s25_PFC_RNA


title: GFP-LC3 oHSC_LO_111

description:
smartseq2
fcounts2.txt


title: s37_PFC_RNA


title: GFP-LC3 oHSC_LO_116

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_HI_111

description:
smartseq2
fcounts2.txt


title: s26_PFC_RNA


title: GFP-LC3 yHSC_107

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_HI_109

description:
smartseq2
fcounts2.txt


title: s31_PFC_RNA


title: GFP-LC3 oHSC_MID_112

description:
smartseq2
fcounts2.txt


title: GFP-LC3 yHSC_106

description:
smartseq2
fcounts2.txt


title: s20_PFC_RNA


title: GFP-LC3 oHSC_MID_110

description:
smartseq2
fcounts2.txt


title: s23_PFC_RNA


title: s22_PFC_RNA


title: GFP-LC3 oHSC_LO_110

description:
smartseq2
fcounts2.txt


title: s19_PFC_RNA


title: GFP-LC3 oHSC_HI_108

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_LO_109

description:
smartseq2
fcounts2.txt


title: s17_PFC_RNA


title: s21_PFC_RNA


title: GFP-LC3 oHSC_MID_109

description:
smartseq2
fcounts2.txt


title: GFP-LC3 yHSC_105

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_HI_107

description:
smartseq2
fcounts2.txt


title: s16_PFC_RNA


title: GFP-LC3 oHSC_LO_108

description:
smartseq2
fcounts2.txt


title: s13_PFC_RNA


title: s15_PFC_RNA


title: s12_PFC_RNA


title: GFP-LC3 oHSC_MID_108

description:
smartseq2
fcounts2.txt


title: s14_PFC_RNA


title: s24_PFC_RNA


title: GFP-LC3 yHSC_104

description:
smartseq2
fcounts2.txt


title: s10_PFC_RNA


title: GFP-LC3 oHSC_HI_106

description:
smartseq2
fcounts2.txt


title: s11_PFC_RNA


title: s8_PFC_RNA


title: s9_PFC_RNA


title: GFP-LC3 oHSC_LO_107

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_MID_107

description:
smartseq2
fcounts2.txt


title: GFP-LC3 yHSC_103

description:
smartseq2
fcounts2.txt


title: s6_PFC_RNA


title: s4_PFC_RNA


title: GFP-LC3 yHSC_102

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_HI_105

description:
smartseq2
fcounts2.txt


title: s5_PFC_RNA


title: s18_PFC_RNA


title: GFP-LC3 oHSC_MID_106

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_MID_105

description:
smartseq2
fcounts2.txt


title: s7_PFC_RNA


title: GFP-LC3 oHSC_HI_104

description:
smartseq2
fcounts2.txt


title: s2_PFC_RNA


title: GFP-LC3 oHSC_LO_106

description:
smartseq2
fcounts2.txt


title: s1_PFC_RNA


title: s3_PFC_RNA


title: MGA-KO Molm13 cells Rep2

city: Memphis

first: Michael

last: Walsh

address: 262 Danny Thomas

institute: St Jude Children's Research Hospital

data_processing:
Raw reads in fastq format were processed with Trim-Galore tool (v0.4.4, Krueger F. (2012)), in order to remove potential adapters and quality trim 3’ end of reads with cutadapt program, followed by FastQC analysis
A quality score cutoff of Q20 was used and the first 15bp of each reads were also clipped to reduce the GC bias. Next, reads were mapped to the human reference genome (hg38; GRCh38.p12) with BWA mem (0.7.17-r1188), then converted to BAM format and deduplicated with fq2bam (v3.0.0.6)
Subsequently, uniquely mapped properly paired reads were extracted with samtools (v1.2), and fragments were extracted with bedtools(v2.24.0)
Assembly: GRCh38 and GRCm38
Supplementary files format and content: BigWig format

growth_protocol: MOLM-13 cells or Lin-,cKit+ HSPCs were harvested at 50,000 cells.

extract_protocol:
Open chromatin status was assessed using the assay for transposase-accessible chromatin via sequencing (ATAC-seq) kit (Active Motif, CA) following the manufacturer’s protocols.
Library prep, included in kit, was done following the manufacturer’s protocols (Active Motif, CA).

tag: cell line

value: AML


title: GFP-LC3 oHSC_LO_105

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_MID_104

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_HI_103

description:
smartseq2
fcounts2.txt


title: MGA-KO Molm13 cells Rep1


title: WT Molm13 cells Rep2


title: GFP-LC3 yHSC_101

description:
smartseq2
fcounts2.txt

value: young


title: GFP-LC3 oHSC_HI_102

description:
smartseq2
fcounts2.txt


title: WT Molm13 cells Rep1


title: GFP-LC3 oHSC_LO_104

description:
smartseq2
fcounts2.txt


title: 2480867_SJNORM079770_C2-CD34_AML_ETO_KO-IGG-AB14

data_processing:
To obtain quality reads, raw reads were processed and trimmed with Trim_galore (v0.4.4) from cutadapt (DOI: 10.14806ej.17.1.200) and FASTQC analysis. A default quality score cutoff of Q20 is used.  Quality trimmed reads were then mapped to "hg38+rDNA” (DOI: 10.1101/2022.11.10.514243) genome build by bwa (v0.7.12-r1039) and converted to a bam file by samtools (v1.2).
Duplicate reads were marked with biobambam2 (v2.0.87, DOI: 10.1186/175109473-9-13). Uniquely mapped and properly paired reads were then extracted with samtools (v1.2, "-F 1804 -q 1") and sorted by read name using biobambam2 (v2.0.87)
bedtools(v2.17.0, PMID: 20110278) were used to convert bam file to bedpe file as fragments. Fragments with size shorter than 2000bp were extracted and center 80bp of each fragment were used to generate bigwig track files by UCSC tools (v4) and visualized using IGV (v2.16.0).
Narrow peaks were called with MACS2 (v2.1.1.20160309, parameters "-q 0.05") and broad peaks were called by SICER (v1.1, parameters "hg38 1 200 fragmentsize 0.86 600 0.00001").
To perform statistical test between experimental groups, fragments for each reference peak were counted with intersect command from pybedtools (v0.9.1). Next, the number of raw reads mapping per peak were converted to FPKM unit (Fragments Per Kilo base per Million mapped reads), and TMM (trimmed mean of M-values) from edgeR package. Next, we used limma-voom approach to assess the significance of differential peak binding.  Significant peaks were defined by log2FC < -1 or > 1 and FDR < 0.05.
Assembly: GRCh38 and GRCm38
Supplementary files format and content: BigWig format
Library strategy: CUT&RUN

extract_protocol:
CUT&RUN was performed following the kit from EpiCypher (cat# 14-1048)
CUT&RUN DNA libraries were made following NEBNext Ultra II DNA Library Prep Kit for Illumina (cat# E7103), PCR amplification was done for 12 cycles

tag: chip antibody

value: anti-IgG, Epicypher 13-0042k


title: GFP-LC3 oHSC_LO_103

description:
smartseq2
fcounts2.txt


title: 2480863_SJNORM079770_C1-CD34_AML_ETO_WT-PCGF6-AB1

value: anti-PCGF6, Proteintech 24103-1-AP


title: 2480868_SJNORM079770_C2-CD34_AML_ETO_KO-MGA-AB1

value: anti-MGA, sigmaaldrich HPA042278


title: GFP-LC3 oHSC_MID_103

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_HI_101

description:
smartseq2
fcounts2.txt


title: 2480870_SJNORM079770_C2-CD34_AML_ETO_KO-PCGF6-AB1


title: GFP-LC3 yHSC_99

description:
smartseq2
fcounts2.txt


title: 2480860_SJNORM079770_C1-CD34_AML_ETO_WT-IGG-AB14


title: 2505024_SJAML079769_C4_Molm13_KO_PCGF6_AB1


title: 2505023_SJAML079769_C4_Molm13_KO_H2AK119ub1_AB1

value: anti-H2AK119Ub1, Cell signaling 8240S


title: 2480861_SJNORM079770_C1-CD34_AML_ETO_WT-MGA-AB1


title: GFP-LC3 oHSC_HI_100

description:
smartseq2
fcounts2.txt


title: 2505025_SJAML079769_C4_Molm13_KO_CMYC_AB2

value: anti-cMYC, CellSignaling #9402


title: GFP-LC3 oHSC_MID_101

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_LO_102

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_MID_102

description:
smartseq2
fcounts2.txt


title: GFP-LC3 yHSC_100

description:
smartseq2
fcounts2.txt


title: 2505021_SJAML079769_C4_Molm13_KO_H3K27Ac_AB5

value: anti-H3K27Ac, Cell signaling 8173S


title: 2505020_SJAML079769_C3_Molm13_WT_CMYC_AB2


title: 2505019_SJAML079769_C3_Molm13_WT_PCGF6_AB1


title: GFP-LC3 oHSC_HI_99

description:
smartseq2
fcounts2.txt


title: GFP-LC3 yHSC_97

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_LO_100

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_MID_100

description:
smartseq2
fcounts2.txt


title: 2505017_SJAML079769_C3_Molm13_WT_H3K27me3_AB4

value: anti-H3K27me3, Cell signaling 9733S


title: GFP-LC3 oHSC_LO_101

description:
smartseq2
fcounts2.txt


title: GFP-LC3 yHSC_96

description:
smartseq2
fcounts2.txt


title: 2505016_SJAML079769_C3_Molm13_WT_H3K27Ac_AB5


title: GFP-LC3 oHSC_HI_98

description:
smartseq2
fcounts2.txt


title: SJAML079769_C2-Molm13_KO-H2AK119ub1-AB1


title: GFP-LC3 oHSC_MID_99

description:
smartseq2
fcounts2.txt


title: SJAML079769_C2-Molm13_KO-H3K4me3-AB12

value: anti-H3K4me3, Epicypher 13-0041


title: GFP-LC3 yHSC_98

description:
smartseq2
fcounts2.txt


title: 2505022_SJAML079769_C4_Molm13_KO_H3K27me3_AB4


title: GFP-LC3 oHSC_MID_98

description:
smartseq2
fcounts2.txt


title: SJAML079769_C2-Molm13_KO-IGG-AB14


title: 2505018_SJAML079769_C3_Molm13_WT_H2AK119ub1_AB1


title: GFP-LC3 yHSC_95

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_HI_97

description:
smartseq2
fcounts2.txt


title: SJAML079769_C1-Molm13_WT-MGA-AB1


title: SJAML079769_C1-Molm13_WT-H2AK119ub1-AB1


title: SJAML079769_C1-Molm13_WT-IGG-AB14


title: SJAML079769_C2-Molm13_KO-MGA-AB1


title: GFP-LC3 oHSC_LO_98

description:
smartseq2
fcounts2.txt


title: GFP-LC3 yHSC_94

description:
smartseq2
fcounts2.txt


title: SJAML076951_C2-Molm13_KO-H2AK119ub1-AB1


title: GFP-LC3 oHSC_HI_96

description:
smartseq2
fcounts2.txt


title: SJAML076951_C2-Molm13_KO-H3K27me3-AB4


title: 2505014_SJAML079769_C3_Molm13_WT_IGG_AB14


title: GFP-LC3 oHSC_MID_97

description:
smartseq2
fcounts2.txt


title: SJAML076951_C2-Molm13_KO-H3K4me3-AB12


title: GFP-LC3 oHSC_LO_97

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_HI_95

description:
smartseq2
fcounts2.txt


title: SJAML076951_C2-Molm13_KO-MGA-AB1


title: GFP-LC3 oHSC_MID_96

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_LO_99

description:
smartseq2
fcounts2.txt


title: SJAML076951_C2-Molm13_KO-PCGF6-AB1


title: GFP-LC3 oHSC_LO_96

description:
smartseq2
fcounts2.txt


title: GFP-LC3 yHSC_92

description:
smartseq2
fcounts2.txt


title: SJAML076951_C2-Molm13_KO-CMYC-AB2


title: SJAML079769_C1-Molm13_WT-H3K4me3-AB12


title: SJAML076951_C1-Molm13_WT-IGG-AB14


title: GFP-LC3 oHSC_HI_94

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_MID_95

description:
smartseq2
fcounts2.txt


title: SJAML076951_C1-Molm13_WT-H2AK119ub1-AB1


title: SJAML076951_C1-Molm13_WT-H3K27me3-AB4


title: SJAML076951_C1-Molm13_WT-H3K27Ac-AB5


title: GFP-LC3 yHSC_91

description:
smartseq2
fcounts2.txt


title: SJAML076951_C1-Molm13_WT-H3K4me3-AB12


title: GFP-LC3 oHSC_HI_93

description:
smartseq2
fcounts2.txt


title: SJAML076951_C2-Molm13_KO-H3K27Ac-AB5


title: GFP-LC3 yHSC_93

description:
smartseq2
fcounts2.txt


title: SJAML076951_C1-Molm13_WT-CMYC-AB2


title: GFP-LC3 oHSC_MID_94

description:
smartseq2
fcounts2.txt


title: GFP-LC3 yHSC_90

description:
smartseq2
fcounts2.txt


title: SJAML076951_C1-Molm13_WT-PCGF6-AB1


title: 2348247_SJAML076231_C1-Molm13_WT-IGG-AB14


title: 2348246_SJAML076231_C2-Molm13_KO-H3K4me3-AB12


title: GFP-LC3 oHSC_HI_92

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_LO_94

description:
smartseq2
fcounts2.txt


title: 2348245_SJAML076231_C2-Molm13_KO-H3K27me3-AB4


title: GFP-LC3 oHSC_LO_93

description:
smartseq2
fcounts2.txt


title: 2348244_SJAML076231_C2-Molm13_KO


title: GFP-LC3 yHSC_89

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_HI_91

description:
smartseq2
fcounts2.txt


title: 2348242_SJAML076231_C1-Molm13_WT-H3K4me3-AB12


title: GFP-LC3 oHSC_MID_92

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_LO_95

description:
smartseq2
fcounts2.txt


title: 2348241_SJAML076231_C1-Molm13_WT-H3K27me3-AB4


title: SJAML076951_C1-Molm13_WT-MGA-AB1


title: GFP-LC3 oHSC_LO_92

description:
smartseq2
fcounts2.txt


title: 2348240_SJAML076231_C1-Molm13_WT-H2AK119ub1-AB1


title: 2294325_SJAML075820_C2-MOLM13_KO-H3K27Ac-AB5


title: 2348239_SJAML076231_C1-Molm13_WT-MGA-AB1


title: GFP-LC3 oHSC_MID_91

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_HI_90

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_LO_91

description:
smartseq2
fcounts2.txt


title: 2294323_SJAML075820_C2-MOLM13_KO-MGA-AB1


title: 2294322_SJAML075820_C1-MOLM13_WT-H3K27Ac-AB5


title: GFP-LC3 yHSC_87

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_HI_89

description:
smartseq2
fcounts2.txt


title: 2348243_SJAML076231_C2-Molm13_KO-MGA-AB1


title: GFP-LC3 oHSC_MID_93

description:
smartseq2
fcounts2.txt


title: GFP-LC3 oHSC_MID_90

description:
smartseq2
fcounts2.txt


title: 2294320_SJAML075820_C1-MOLM13_WT-MGA-AB1


title: GFP-LC3 oHSC_LO_90

description:
smartseq2
fcounts2.txt


title: 2294321_SJAML075820_C1-MOLM13_WT-H3K4me3-AB12